The two explosions on Wednesday -- labelled a "terrorist attack" by Iran's state media and regional authorities -- sparked fears of a widening conflict in the region.
Iranian authorities on Thursday said the blasts had killed 84 people, revising down an earlier toll of 95.
In a message to Raisi, Xi said he was "shocked to learn of the serious terrorist attack in Iran's Kerman province, which resulted in heavy casualties", state broadcaster CCTV reported.
"On behalf of the Chinese government and people, I would like to express our deep condolences to the victims and our sincere sympathy to the injured and the families of the victims," he was reported as saying.
Xi "stressed that the Chinese side opposes all forms of terrorism, strongly condemns terrorist attacks and firmly supports Iran's efforts to maintain national security and stability", according to CCTV.
Beijing's foreign ministry earlier expressed "deep shock" and condolences over the blasts.
Iran blamed the explosions on Israel and the United States and its supreme leader Ayatollah Ali Khamenei has vowed a "harsh response".
The United States has denied involvement.
Beijing did not say who it believed was responsible for the attack.
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