This study investigated the differences in morphometry and functional plasticity characteristics of the brain after long-term training of different intensities. Results showed that an aerobic group demonstrated higher gray matter volume in the cerebellum and temporal lobe, while an anaerobic group demonstrated higher gray matter volume in the region of basal ganglia. In addition, the aerobic group also showed significantly higher fractional amplitude of low-frequency fluctuation (fALFF) and degree centrality (DC) in the motor area of the frontal lobe and parietal lobe, and the frontal gyrus, respectively. At the same time, the anaerobic group demonstrated higher fALFF and DC in the cerebellum posterior lobe (family-wise error corrected, < 0.01). These findings may further prove that different brain activation modes respond to different intensities of physical activity and may help to reveal the neural mechanisms that can classify athletes from different intensity sports.