BACKGROUND: Motor control exercise (MCE) is effective in alleviating non-specific chronic low back pain (NCLBP). Neuro-imaging research is warranted to explore the underlying neural mechanisms of MCE. AIM: We used resting-state functional magnetic resonance imaging (rs-fMRI) to explore the central mechanism underpinning the effects of MCE in patients with NCLBP. DESIGN: A randomized, single-blinded, controlled trial. SETTING: The setting was out-patient and community. POPULATION: Fifty-eight patients with NCLBP. METHODS: Patients were randomized into the MCE or manual therapy (MT) group. All the participants completed pain-related clinical assessments and rs-fMRI scans before and after intervention. We performed exploratory whole-brain analyses in regional homogeneity (ReHo) and resting-state functional connectivity (rsFC) with significant post-pre differences in ReHo before and after intervention, and investigated associations between imaging and pain-related clinical assessments. RESULTS: Compared with the MT group, a greater alleviation in pain intensity and disability was observed in the MCE group after intervention, and was sustained at the 6-month follow-up (P<0.001). Only the MCE group showed increased ReHo values in the right pre-central gyrus and decreased ReHo values in the bilateral posterior cerebellum (voxel level P<0.001, cluster-level FWE corrected P<0.05). Decreased rsFC of the right posterior cerebellum-left superior parietal gyrus and left insula were significantly positively associated with pain-related disability (voxel level P<0.001, cluster-level FWE corrected P<0.05). CONCLUSIONS: These findings demonstrated that MCE had superior effects in relieving pain and pain-related disability, which might be associated with its modulation of rsFC between the cerebellum and areas involved in sensory-discriminative processing of noxious and somato-sensory stimuli, affection, and cognition. CLINICAL REHABILITATION IMPACT: This study provided preliminary evidence that MCE might alleviate NCLBP through its modulation of the function of brain areas related to chronic pain and postural control. Those results support MCE's clinical application and help physiotherapists to provide better multidisciplinary interventions with the combination of MCE and other first-line treatments.