In this study, we explored the neural mechanism underlying impaired stereopsis and possible functional plasticity after strabismus surgery. We enrolled 18 stereo-deficient patients with intermittent exotropia before and after surgery, along with 18 healthy controls. Functional magnetic resonance imaging data were collected when participants viewed three-dimensional stimuli. Compared with controls, preoperative patients showed hypoactivation in higher-level dorsal (visual and parietal) areas and ventral visual areas. Pre- and postoperative activation did not significantly differ in patients overall; patients with improved stereopsis showed stronger postoperative activation than preoperative activation in the right V3A and left intraparietal sulcus. Worse stereopsis and fusional control were correlated with preoperative hypoactivation, suggesting that cortical deficits along the two streams might reflect impaired stereopsis in intermittent exotropia. The correlation between improved stereopsis and activation in the right V3A after surgery indicates that functional plasticity may underlie the improvement of stereopsis. Thus, additional postoperative strategies are needed to promote functional plasticity and enhance the recovery of stereopsis.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12264-022-00987-7.