Background: Cognitive behavioural therapy (CBT) is considered an effective first-line treatment for obsessive–compulsive disorder (OCD). However, the neural basis of CBT for OCD has not yet been elucidated. The role of the amygdala in OCD and its functional coupling with the cerebral cortex have received increasing attention, and may provide new understanding of the neural basis of CBT for OCD. Methods: We ac- quired baseline resting-state functional MRI (fMRI) scans from 45 unmedicated patients with OCD and 40 healthy controls; we then acquired another wave of resting-state fMRI scans from the patients with OCD after 12 weeks of CBT. We performed seed-based resting-state functional connectivity analyses of the amygdala subregions to examine changes in patients with OCD as a result of CBT. Results: Compared to healthy controls, patients with OCD showed significantly increased resting-state functional connectivity at baseline between the left basolateral amyg- dala and the right middle frontal gyrus, and between the superficial amygdala and the right cuneus. In patients with OCD who responded to CBT, we found decreased resting-state functional connectivity after CBT between the amygdala subregions and the visual association cortices and increased resting-state functional connectivity between the amygdala subregions and the right inferior parietal lobe. Furthermore, these changes in resting-state functional connectivity were positively associated with changes in scores on the compulsion or obsession subscales of the Yale–Brown Obsessive–Compulsive Scale. Limitations: Because of the lack of a second scan for healthy controls after 12 weeks, our re- sults may have been confounded by other variables. Conclusions: Our findings yield insights into the pathophysiology of OCD; they also re- veal the potential neural changes elicited by CBT, and thus have implications for guiding effective treatment strategies with CBT for OCD.