Magnetic stimulation has a potential therapeutic effect on patients with chronic nonspecific low back pain (CNLBP). However, the efficacy and underlying brain mechanisms of closed-loop magnetic stimulation for CNLBP remain unclear. This study aims to investigate the analgesic efficacy and brain activation of repetitive transcranial magnetic stimulation (rTMS) combined with repetitive peripheral magnetic stimulation (rPMS) in patients with CNLBP. This was a single-center, double-blind, randomized controlled trial. Huashan Hospital. CNLBP. Thirty patients with CNLBP were randomly allocated into the experimental group and control group, with fifteen patients in each group. Patients in both groups received CNLBP-related health education. On this basis, patients in the experimental group received a two-week rTMS combined with rPMS treatment, while the control group received rPMS treatment combined with sham-rTMS stimulation. Visual analogue scale (VAS), Oswestry Disability Index (ODI), and Neurometer CPT sensory nerve quantitative detector were used to evaluate the participants before and after treatment. In addition, functional near-infrared imaging (fNIRS) was employed to ascertain participants' brain function. After treatment, both groups exhibited a significant decrease in VAS and ODI scores compared to their pre-treatment levels (all P<0.05). While there was no statistical significance between the two groups. Neurometer CPT revealed that the experimental group improved the pain threshold of C-fiber on the unaffected side (P=0.036). In addition, compared with the control group, the experimental group exhibited a notable increase in the activation of the somatosensory association cortex (SAC) region and an improvement in the functional connectivity of brain regions, including SAC and the primary motor cortex (PMC), after treatment. Combining rTMS with rPMS can significantly relieve pain and remodel brain regions in individuals with CNLBP. This closed-loop rehabilitation model paradigm merits additional clinical investigation and implementation. Magnetic stimulation therapy based on closed-loop rehabilitation mode has a good prospect for clinical rehabilitation for patients with CNLBP.