Now as an international court prepares to hand down a ruling that threatens China's sweeping claims in the vital waterway, Beijing is watching Clinton's presidential run with trepidation.
Combined with her tough line on human rights and role in leading President Barack Obama's Asia "rebalancing", Clinton is well-known in China - but not well liked.
While presidential rival Donald Trump has irritated Beijing with comments such as comparing the U.S. trade deficit with China to rape, he is largely an unknown quantity, a person who even privately officials shrug their shoulders over.
"Clinton will be a difficult partner," one senior Chinese diplomatic source told Reuters, having just admitted to not knowing much about Trump or what he stands for.
China remembers clearly a 2010 Southeast Asian security summit in Hanoi, when Clinton waded into the South China Sea dispute, saying open access and legal solutions were a U.S. "national interest" and "pivotal to regional security".
In a strongly worded response, China stressed the South China Sea as one of its "core interests", putting the issue up there with Taiwan, Tibet and Xinjiang in terms of its importance to Beijing.
China warned its rival claimants and neighbors not to be emboldened by U.S. support - a line it has repeated ever since.
An arbitration court hearing the dispute between China and the Philippines over the South China Sea is set to hand down its ruling on in the Dutch city of The Hague on Tuesday. Legal experts expect at least some substantive findings to go against China, which has vowed to ignore the ruling.
STRENGTH, RESPECT
China's military, which is ramping up its presence in the South China Sea as part of a major modernization program, is also watching the election closely.
"Hillary is very fierce when it comes to China," a Chinese official close to the military establishment told Reuters.
While the Chinese government has been largely quiet about the U.S. election, state media has not been so restrained, with one paper even equating Trump to Hitler.
In May, China's official Xinhua news agency noted Trump's more isolationist campaign compared to Clinton's, who it described as an "old foreign policy hand" and important backer of the Asia-Pacific "pivot" that China considers a threat.
"As far as she's concerned, being tough on foreign policy is perhaps the best way to show America's so called 'leadership'," it said in a commentary.
Laura Rosenberger, a Clinton campaign foreign policy adviser who worked with her in the State Department, told Reuters Clinton would remain tough on the South China Sea issue.
"She believes that we need to be very strong in terms of standing up to many of the actions the Chinese have taken," Rosenberger said.
"She believes in the principles of freedom of navigation in international waters, that commerce on the high seas in incredibly important to the United States, and that these are really very direct interests that we need to continue to stand up for."
Trump adviser Peter Navarro, an economist at University of California Irvine and the author of the book, "Crouching Tiger: What China's Militarism Means for the World," said a Trump presidency would lead to respect.
"The central difference between a Trump administration and the current administration or a Clinton administration is respect. The leaders of Russia, the leaders of China will respect Mr. Trump, will respect America because we will be strong economically, militarily and politically."
UNKNOWN QUANTITY
Trump may actually find some sympathy in China, even if he is seen as an unknown quantity.
"Who is Trump? We don't really know. We do know he hates Muslims though - and that will be well received in some circles here," said the Chinese official with ties to the military, pointing to what China views as its war on terror in its Muslim-populated far western region of Xinjiang.
China also views Trump as a businessmen with whom they can probably negotiate.
"It would be very transactional for the Chinese," said a senior Western diplomat in Beijing. "He's a businessman they think they'll be able to strike a deal with."
Trump may also be less tough on China over human rights than Clinton, who has frequently clashed with Beijing on the issue.
In 2011, Clinton said China was on a "fool's errand" to try to halt the march of freedom, while in 2012 she was deeply involved in efforts to get blind dissident Chen Guangcheng out of China after he fled to the U.S. embassy in Beijing.
Trump advisor Navarro said Clinton's record on human rights abuse was "sketchy at best and abysmal at worst", highlighting her first trip to Asia as Secretary of State in 2009, where other issues were given priority.
"So it's difficult to see how she would have someone would view her as credible on that issue."
Rosenberger, the Clinton adviser, rejected that view, highlighting comments from Trump in a 1990 interview referring to the "strength" of the Chinese government in its bloody crackdown of student-led protests in Tiananmen Square a year earlier.
“It’s ironic for Trump’s adviser to criticize Hillary’s statement there when Trump himself has actually praised the Chinese for the Tiananmen massacre,” Rosenberger said.
Still, China is hoping that whoever wins they will understand that both countries need each other and will have to work closely, a source with ties to the Chinese leadership told Reuters, requesting anonymity.
"It is the most important bilateral relationship in the world. China needs the United States and vice versa," the source said. "We don't know who will be the lesser of two evils."
(Additional reporting by Benjamin Kang Lim and Michael Martina in Beijing, Greg Torode in Hong Kong, and Alana Wise and Caren Bohan in Washington)
