Ms Clinton arrived after talks in Indonesia which focused on territorial disputes in the South China Sea.
In Indonesia she urged regional bloc Asean to form a united front on the issue.
Ms Clinton and Chinese officials are also expected to discuss Syria, Iran and North Korea.
She arrived in Beijing late on Tuesday and will spend all of Wednesday meeting senior officials.
After China she is scheduled to visit East Timor and Brunei before heading to the Apec forum in Russia as part of her 11-day tour.
Territorial rows
Ahead of Ms Clinton's arrival, the Chinese foreign ministry expressed its hope that the US would maintain its previously stated position of neutrality over the South China Sea disputes.
"We hope the US side will keep its commitment and make efforts that help, rather than harm, regional peace and stability," foreign ministry spokesman Hong Lei told reporters.
In addition, one state-run newspaper has accused the secretary of state of causing profound mistrust between the two countries.
In talks at the headquarters of the Association of South-East Asian Nations (Asean) in the Indonesian capital Jakarta, Ms Clinton called on Asean countries to stand together on the issue and pushed for a code of conduct governing maritime territorial disputes.
China has competing territorial claims with four Asean member-states in the South China Sea. The rows have led to increased tensions in the region.
Earlier this year, vessels from China and the Philippines faced off for several weeks over one area, the Scarborough Shoal.
Mrs Clinton said on Tuesday that the US had a national interest in maintaining peace, stability and respect for international law in the region.
While the US "does not take a position on competing territorial claims", she said, "we believe the nations of the region should work collaboratively to resolve disputes without coercion, without intimidation and certainly without the use of force".
At a regular meeting hosted by Cambodia in July, Asean failed for the first time in its 45-year history to issue a joint statement because of tensions over the disputes.
Vietnam and the Philippines accused host Cambodia of yielding to Chinese pressure to keep the issue off the agenda.
'Strong opposition'
Chinese media has been lukewarm ahead of her visit.
"Though US Secretary of State Hillary Clinton has said the Asia-Pacific is big enough to hold both China and the United States, Washington still need to take concrete actions to improve its ties with China," an article on state-run Xinhua news agency said.
"Moreover, Washington has been trying to work with a number of South East Asian nations to force China into a multi-national solution to territorial rows in the South China Sea, despite China's strong and perennial opposition."
Mrs Clinton's last visit to China in 2 May was overshadowed by the diplomatic crisis over the blind Chinese activist Chen Guangcheng, who fled to the US embassy.
He was later allowed to go to New York to study.-British Broadcasting Corporation (September 04, 2012)
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