The statement comes a day after Trump ordered additional tariffs against Chinese goods, increasing previously imposed 10 percent levies to 20 percent.
"The United States' unilateral tax measures seriously violate WTO rules and undermine the foundation of China-US economic and trade cooperation," Beijing's commerce ministry said in a statement, adding that it was "strongly dissatisfied and firmly opposed" to the tariffs.
In response to the US tariffs, Beijing has imposed new duties on a range of agricultural imports from the United States.
The additional 15 percent tariffs on products including chicken, wheat, corn and cotton are due to come into effect next week.
"China will, in accordance with WTO rules, firmly safeguard its legitimate rights and interests and defend... the international economic and trade order," the commerce ministry statement added.
A WTO official confirmed to AFP that the new complaint from China had been received.
Trump, in imposing the tariffs, said China had not done enough to halt the trafficking of fentanyl and other highly potent opioids that kill thousands of Americans each year.
Analysts say that stemming the flow of deadly drugs is just one aim for Trump, who also frequently mentions trade imbalances when discussing the tariffs.
In a white paper released Tuesday, China's National Narcotics Control Commission touted actions already taken to crack down on trafficking of fentanyl-related substances, state media reported.
"Since implementing full control of fentanyl-related substances, China has not detected any further cases of smuggling or selling fentanyl-related substances abroad," Xinhua reported, attributing the matter to a senior commission official.
China is a major market for US energy exports and according to Beijing customs data, imports of oil, coal and LNG totalled more than $7 billion last year.
Beijing launched a similar dispute in February when Trump first threatened the tariffs, describing the levies as "malicious" at the time.
It says it will also probe US tech giant Google and the American fashion group which owns Tommy Hilfiger and Calvin Klein.
Trump has made tariffs a key foreign policy tool of his second term, joking that the word tariff is the "most beautiful" in the dictionary.
The Republican has also imposed tariffs on Mexico and Canada which he says are punishment for failing to halt the flow of migrants and drugs into the United States.
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