The invention discloses a method and a system for rebuilding a three-dimensional head model by two-dimensional nuclear magnetic images. The method includes the steps: preprocessing the two-dimensional nuclear magnetic images of a human head, and removing noise on the two-dimensional nuclear magnetic images; acquiring all non-empty voxels on two adjacent denoised two-dimensional nuclear magnetic images; searching intersection relations among the non-empty voxels and contour surfaces, and selecting middle points of intersection edges of the non-empty voxels and the contour surfaces to serve as intersection points of the non-empty voxels and the contour surfaces; sequentially connecting all intersection points of each non-empty voxel and the contour surfaces to form a three-dimensional polygonal facet; connecting the three-dimensional polygonal facets formed by intersecting the non-empty voxels and the contour surfaces to form the three-dimensional head model. The method and the system for rebuilding the three-dimensional head model by the two-dimensional nuclear magnetic images are high in rebuilding accuracy and efficiency and small in calculated amount, and the rebuilding performance of the three-dimensional model of the human head is integrally improved.