The "unprecedented weather events" have compounded suffering in the Arabian Peninsula's poorest country, which is already grappling with one of the world's worst humanitarian crises, said the IOM.
"The scale of the destruction is staggering, and we urgently need additional funding to ensure that the most vulnerable are not left behind," said Matt Huber, the IOM's acting Yemen mission chief.
Since late July, torrential rains and flooding have destroyed homes, displaced thousands of families and severely damaged critical infrastructure, including health centres, schools and roads, according to the UN agency.
Late last month, torrential rains caused flash floods in Yemen's Mahawit governorate, leaving around 40 people either missing or dead, according to the UN's humanitarian agency OCHA.
Dozens of houses were damaged or destroyed, forcing 215 families into displacement, it said.
Another 60 people were killed and hundreds more were injured in earlier flash floods across Yemen since late July, according to UN figures.
"These rains have not only led to tragic loss of life but have also wiped out entire communities' belongings and means of survival," the IOM said.
"Immediate funding is necessary to address the most pressing needs on the ground," the IOM said, warning that severe weather conditions are expected to continue in the coming weeks.
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