The neural basis underlying stereopsis defects in patients with amblyopia remains unclear, which hinders the development of clinical therapy. This study aimed to investigate visual network abnormalities in patients with amblyopia and their associations with stereopsis function. Spectral dynamic causal modeling methods were employed for resting-state functional magnetic resonance imaging data to investigate the effective connectivity (EC) among 14 predefined regions of interest in the dorsal and ventral visual pathways. We adopted two independent datasets, including a cross-sectional and a longitudinal dataset. In the cross-sectional dataset, we compared group differences in EC between 31 patients with amblyopia (mean age: 26.39 years old) and 31 healthy controls (mean age: 25.71 years old) and investigated the association between EC and stereoacuity. In addition, we explored EC changes after perceptual learning in a novel longitudinal dataset including 9 patients with amblyopia (mean age: 15.78 years old). We found consistent evidence from the two datasets indicating that the aberrant EC from V2v to LO2 is crucial for the stereoscopic deficits in the patients with amblyopia: it was weaker in the patients than in the controls, showed a positive linear relationship with the stereoscopic function, and increased after perceptual learning in the patients. In addition, higher-level dorsal (V3d, V3A, and V3B) and ventral areas (LO1 and LO2) were important nodes in the network of abnormal ECs associated with stereoscopic deficits in the patients with amblyopia. Our research provides insights into the neural mechanism underlying stereopsis deficits in patients with amblyopia and provides candidate targets for focused stimulus interventions to enhance the efficacy of clinical treatment for the improvement of stereopsis deficiency.