Foreign ministry spokesman Lu Kang charged that the legislation, while non-binding, violates the one-China policy and "constitutes an interference in China's domestic affairs".
"We firmly oppose any form of official exchanges or military links between Taiwan and the US, as well as US arms sales to Taiwan," Lu told a regular news briefing.
"We hope that the US can fully grasp the damaging nature" of the legislation's Taiwan clause, he said.
Trump on Tuesday signed the budget, which includes a clause saying the United States should "consider the advisability and feasibility of reestablishing port of call exchanges between the United States navy and the Taiwan navy".
Chinese media reported last week that a diplomat from the Chinese embassy in the United States had warned that Beijing would take Taiwan back by force the day that a US warship enters a Taiwanese port.
The island has been a thorny issue in China-US relations, as Trump began his transition into office by taking a precedent-breaking phone call from Taiwanese president Tsai Ing-wen.
Trump mended ties by vowing to uphold the one-China policy shortly before Chinese President Xi Jinping's visit to his Florida Mar-a-Lago resort, but infuriated Beijing again this summer by approving a $1.3 billion arms sale to Taiwan.
China and Taiwan split after a civil war in 1949, and while Taiwan sees itself as a sovereign nation, it has never formally declared independence.
Beijing says Taiwan is a part of Chinese territory and will be brought back into the fold at some point.
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