Objective The aim of this study was to evaluate the recovery about the visual cortex function of stereopsis in anisometropic amblyopia after regular amblyopia treatment with blood oxygenation level dependent functional MRI techniques (BOLD-fMRI).Methods In this study,selfcontrolled study before and after treatment was used,and blocks-designed fMRI was performed on 11 children with first amblyopic treatment,and review BOLD-fMRI inspection after regular amblyopia treatment 1 week,2 weeks and 1 month.Functional MRI data were processed by using SPM8 which based on the MATLAB7.12.0.635.Random effect group analysis was performed in each group to acquire average cerebral cortex activated functional images data.Through the hypothesis drive method,the differences range of activated area in each group were compared by before and after amblyopia treatment matched t-test.During the study,the patients were asked to view stimuli through red-blue filtered stereo glasses.The visual stimuli were computer-generated random-dot stereograms (R.D.S),click feedback key immediately after the R.D.S were recognized.Results The functional area that was left occipital lobe (BA18),middle occipital gyrus (BA19),limbic lobe (BA19),lingualis gyrus of the right occipital lobe (BA17) and the bilateral parietal lobe (BA7) expanded in different levels after 4 weeks (compared the fourth weeks with without treatment,mean t value was 1.636,1.902,1.727,1.350 and 1.777 respectively,P＜0.01).However,those data showed activation on the small area,and with the R.D.S on the recovery is not parallel.Conclusion In children anisometropic amblyopia,the visual cortical functional mediating stereopsis is damaged seriously and not easy to treat in the short time.