BACKGROUND: There are various therapeutic options for the conservative management of lower back pain (LBP). A combination of two or more treatment options may be more effective in the clinical management of non-specific LBP. In this study, we compared the effects of simultaneous heat massage with conventional physical therapy in patients with subacute LBP. METHODS: A single-center randomized controlled trial in which 40 participants with LBP were allocated to one of two groups: a heat massage group (HMG) and physical therapy group (PTG). The HMG received simultaneous heat massage therapy using a mechanical device (CGM MB-1401, Ceragem, Republic of Korea). The PTG received conventional physical therapy. Both groups received 40 min of therapy once daily, five times a week, for a total of four weeks. Changes in serum cortisol, epinephrine (EP), and norepinephrine (NE) were assessed. The outcomes were measured using the pain numeric rating scale (PNRS), the Oswestry disability index (ODI), the Roland-Morris disability questionnaire (RMDQ), the short-form McGill pain questionnaire (SF-MPQ), the multidimensional fatigue inventory (MFI-20), the Beck depression inventory (BDI), surface EMG (sEMG), and sympathetic skin response (SSR) at baseline (PRE), at 2 (2 W) and 4 weeks (4 W) following the intervention. RESULTS: The serum EP and NE levels in the HMG decreased after treatment. The PNRS, ODI, RMDQ, and SF-MPQ scores improved without significance in both groups. The BDI score showed improvement in the HMG before the PTG. The MFI-20 score improved in both groups, but the results were better in the HMG than in the PTG at 4 W. All the activities of sEMG were significantly decreased in both groups. However, the improvement of the %MVIC in the HMG was better than that in the PTG at 4 W. The SSR latency on sEMG decreased while the amplitude increased in the HMG at 2 W and 4 W, respectively. CONCLUSIONS: Following 4 weeks of combined therapies, heat massage was not superior to conventional physical therapy alone. Both treatments were shown to be effective in improving LBP and pain-related disability. However, heat massage was shown to have a better effect on the control of autonomic nerve function and underlying moods.