This represents a 172 percent rise on 2016, the US International Rescue Committee said in its report on the Sahel region.
The three countries are facing a deadly jihadist insurgency which began in Mali more than a decade ago, and most of the central Sahel "is highly exposed to changes in climate", it warned.
The report said temperatures are rising 1.5 times faster than the rest of the world with an increase of between two and 4.3 degrees Celsius projected by 2080.
Dry seasons are becoming longer in parts of the Sahel, and rainfall more intense and erratic, meaning droughts and floods are set to intensify, it said.
There is a "vicious cycle of climate change and armed conflict", and the crisis disproportionately affects women, the NGO added.
Nearly three million people have been displaced, including two million just in Burkina Faso, it said.
The report placed blame on French colonial-era authorities, who "neglected" developing peripheral areas and introduced disruptive border controls, as well as post-independence governments.
"Political decisions dating from the French colonial rule through the early 2000s have marginalised peripheral areas of the Central Sahel states both economically and politically," the report said.
"As a result, the populations of these regions face widespread poverty, are particularly dependent on sectors vulnerable to climate change and are more likely to be exposed to armed conflict.
"They therefore suffer a disproportionate burden of the compound crisis."
The NGO also says "frequent military coups", 17 in the region since 1960, have disrupted economic policy and led governments to concentrate their spending on defence.
The NGO called for immediate aid and investment in humanitarian access.
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