A method and system for drawing a brain functional atlas. The method includes: initializing a brain functional atlas of an individual by using a brain functional atlas template to obtain an initial individualized brain functional atlas; dividing the initial individualized brain functional atlas into a plurality of large areas, each large area including a plurality of functional areas; entering iteration, each iteration process including calculating the connection degree between each voxel in each large area and each functional area in the large area in sequence, and adjusting each voxel to the functional area having the highest connection degree with the voxel until all voxels are adjusted; and when an ending condition is satisfied, ending the iteration to obtain a final individualized brain functional atlas.