The American destroyer USS John McCain moved through the waters near the Spratly Islands of Vietnam in free navigation.
"This freedom of navigation is intended to support the legal rights, freedoms and uses of the sea, recognized in international law," the US Navy's Pacific Fleet said in a statement.
The move comes after the US military last week warned it would be "more determined" in its confrontation with China.
The United States recently sent ships to the South China Sea to conduct "free of navigation" activities more frequently, in an attempt to challenge China's irrational claims in the region.
In the statement of the USS John McCain's operations, the US Pacific Fleet Command said that "illegal and expanding maritime claims in the South China Sea pose a serious threat to that freedom.
Vietnam has repeatedly condemned China's illegal activities in the South China Sea.
The administration of US President Donald Trump is said to be trying to "blow" on China in the final weeks of term, after a year of tensions and bilateral relations on the brink of "New Cold War" due to a series of problems.