The two countries are trying to hammer out a trade deal weeks ahead of a March deadline when US tariffs on Chinese goods are scheduled to increase.
The two warships entered China's territorial seas around the Nansha Islands without permission from the Chinese government, ministry spokeswoman Hua Chunying said at a daily news briefing.
The US and its allies periodically send planes and warships near South China Sea islands and reefs claimed by Beijing to signal their right under worldwide law to pass through the waters, invariably angering China. The archipelago lies off the coasts of the Philippines, Malaysia, and southern Vietnam.
Other regional nations-such as the Philippines and Vietnam-lay claim to part of the waterway and the US routinely pushes back against China by sending ships to patrol the sea.
Another US warship, USS McCampbell, sailed within 12 nautical miles (22 kilometres) of the Paracel Islands chain - north of the Spratly Islands - on January 7 during a previous round of trade talks between the two countries.
Communist superpower China claims ownership over nearly all of the South China Sea - frequently slamming the United States and its allies for naval operations in the territory.
Shortly after that operation, China accused the United States of trespassing in its territorial waters - and said it had deployed missiles "capable of targeting medium and large ships".
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters, where Chinese, Japanese and some South-east Asian navies operate.
Tensions came to the fore in September, when a Chinese warship and US destroyer came within 45 yards of collision in the waters, renewing concerns about the risk of US-China confrontation.
Over the last five years China has rapidly built artificial islands housing significant military infrastructure on what had been low-lying reefs.
China says the construction is necessary for defence, and it was the United States that was responsible for tensions by sending warships and military planes close to islands Beijing claims.