BackgroundThe relationship between sedentary time, physical activity, and chronic back pain remains unclear. The study aims to investigate whether sedentary time and physical activity predict chronic back pain and morphological brain changes.MethodsThis cohort study recruited adults aged 37–73 years enrolled between 2006 and 2010, with follow-up until 2014. The total cohort comprised 33,402 participants (mean age: 54.53). Data were collected on daily sedentary time, physical activity, lifestyle factors, and health outcomes.ResultsAfter nearly 8-year follow-up, 3,006 individuals (9.00%) reported chronic back pain in total. Individuals with daily sedentary time exceeding 6 h had a 33% higher risk of chronic back pain compared to those with sedentary time of 2 h or less (RR, 1.33, 95%CI, 1.17–1.52). Sedentary time was also associated with decreased grey matter volume in several brain regions, including bilateral primary somatosensory cortex (S1), secondary somatosensory cortex, putamen, primary motor cortex (M1), insula, hippocampus, amygdala, as well as right supplementary motor area, left medial frontal cortex, and right anterior cingulate cortex (FDR-corrected p-value < 0.05). Compared to individuals who sat for more than 6 h with light physical activity, those engaging in moderate physical activity with sedentary time of 2 h or less (RR, 0.71, 95%CI, 0.52–0.99) exhibited a significant decrease in chronic back pain risk. In addition, replacing sedentary time with equivalent amount of physical activity also demonstrated a reduction in the risk of chronic back pain (RR, 0.87, 95%CI, 0.77–0.99) and increased the reginal grey matter volumes including the amygdala, insula, M1, putamen and S1.ConclusionsProlonged sedentary time is associated with heightened risks of chronic back pain and deterioration in brain health.