China "expresses its grave concern over the ongoing Israeli military operations in Rafah", foreign ministry spokeswoman Mao Ning said.
The UN Security Council is set to convene an emergency meeting Tuesday over Israel's operations in the southern Gaza border city.
An Israeli attack targeting two senior Hamas members on Sunday night sparked a fire that ripped through a displacement centre, killing 45, according to Gaza health officials.
The attack prompted a wave of international condemnation, with Palestinians and many Arab countries calling it a "massacre". Israel said it was looking into the "tragic accident".
On Tuesday, Beijing urged "all parties to protect civilians and civilian facilities".
It also said it "strongly urges Israel to listen to the appeals of the international community and to stop its attacks on Rafah".
Beijing has been calling for an immediate ceasefire since the start of the current Israel-Hamas war in October last year.
China has historically been sympathetic to the Palestinian cause and supportive of a two-state solution to the Israeli-Palestinian conflict.
And President Xi Jinping has called for an "international peace conference" to resolve the fighting.
The war in Gaza started after Hamas's October 7 attack on southern Israel, which resulted in the deaths of more than 1,170 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Militants also took 252 hostages, 121 of whom remain in Gaza, including 37 the army says are dead.
Israel's retaliatory offensive has killed at least 36,050 people in Gaza, mostly civilians, according to the Hamas-run territory's health ministry.
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