As a prevalent spine disorder, Lumbar disc herniation (LDH) has been affecting more than 2 % of the worldwide population and is characterised by uncertain causes and recurring episodes. Studying the brain activity of patients could potentially provide insights into its pathogenesis and significantly enhance therapy. Therefore, we here examined brain function in patients under Spinal Manipulative Therapy (SMT). By analysing regional homogeneity (ReHo) at different frequency bands, we identified the discrepancies in brain activity between LDH patients and healthy people, highlighting the frequency dependence of spontaneous low-frequency oscillations among patients with LDH. Choosing seeds based on the peak ReHo differences helped to elucidate the functional connectivity alterations in the brain regions of LDH. Overall, this study showed that SMT significantly reduced pain, improved dysfunction, and partially rectified aberrant local consistency and functional connection in patients with LDH, not only offering insights into the pathophysiology of LDH from a neurological standpoint, but also providing inspiration for the development of new therapies based on neurobiology.