Objective: To detect the pathogenetic mechanism of motion-sensitive cortical deficit in response to motion stimuli in children with anisometropic amblyopia using a blood oxygenation level-dependent functional magnetic resonance imaging technique (BOLD-fMRI). Methods: This was a case series study. Patients were collected from June to December 2017 at Tianjin Eye Hospital. Twenty-five patients who were diagnosed with anisometropic amblyopia as amblyopia group and twenty-five normal volunteers were examined as control group. A BOLD-fMRI technique on a 1.5T MRI and a horizontally moving sinusoidal grating block design were used for task conditions. All data were processed with SPM5 software, were analyzed by t test. Results: Significant fMRI activation and comparable right and left eye activation were found in the middle temporal area (MT), and Brodmann areas 19 and 37, in all control subjects; Lesser cortical activation in area MT and Brodmann areas 37, 19, and greater activation in the frontal gyrus of the lazy eye group were detected compared to the control group. Lesser cortical activation in Brodmann area 37, 18 of the contralateral eye of the amblyopic group was detected compared to the control group. Lesser cortical activation in area MT and Brodmann areas 19, 18, and greater activation in the frontal lobes of the anisometropic amblyopic eyes were detected compared to the contralateral eyes. Conclusions: The spatial extent and intensity of the visual cortex activation in the visual cortex decreases in the amblyopic eye compared to the normal control. Decreased cortical activation in the fellow eye is prevalent. A greater visual cortex area is activated when stimulating the amblyopic eye.