Objective To evaluate the clinical efficacy of Zhonggu granules combined with governor vessel moxibustion in the treatment of ankylosing spondylitis. Methods A total of 128 patients with ankylosing spondylitis admitted to Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine from January 2022 to August 2023 were selected and were divided into an experimental group and a control group by coin tossing, with 64 cases in each group. In the control group, there were 33 males and 31 females, aged (34.89±8.21) years, and the course of disease was (8.29±4.63) years. In the experimental group, there were 32 males and 32 females, aged (34.56±8.43) years, and the course of disease was (8.34±4.57) years. The control group received conventional drug treatment, oral salazosulfapyridine enteric-coated tablets (1.0 g each time, twice a day) + celecoxib capsules (0.2 g each time, once a day). The experimental group received Zhonggu granules (10 g each time, twice a day, infused with warm water) combined with governor vessel moxibustion (100 min each time, once a week). The treatment course was 3 months. The Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Function Index (BASFI), traditional Chinese medicine (TCM) symptom score, inflammatory polarization indicators [M1 macrophage CD86 expression, M2 macrophage CD16 expression, matrix metalloproteinase 3 (MMP-3), and tumor necrosis factor (TNF)-α], bone metabolism indicators [N-terminal propeptide of type I procollagen (PINP), serum β-C-terminal telopeptide of type I collagen (β-CTX), and bone-specific alkaline phosphatase (BALP)], physical examination indicators (finger-to-floor distance, chest expansion, and occiput-to-wall distance), and clinical efficacy were compared between the two groups. Statistical methods included t test and χ2 test. Results After 3 months of treatment, the BASDAI, BASFI, and TCM symptom score of the experimental group were (2.82±0.40) points, (3.38±0.48) points, and (2.91±0.34) points, which were lower than those of the control group [(4.05±0.58) points, (4.26±0.61) points, and (4.64±0.66) points], with statistically significant differences (t=13.966, 9.070, and 18.642, all P<0.001). There were statistically significant differences in the M1 macrophage CD86 expression, M2 macrophage CD16 expression, and levels of MMP-3, TNF-α, PINP, β-CTX, and BALP between the two groups (t=2.761, 4.094, 4.245, 9.505, 4.056, 3.536, and 4.356, all P<0.05). The finger-to-floor distance, chest expansion, and occiput-to-wall distance of the experimental group were (16.24±3.04) cm, (5.11±0.94) cm, and (2.76±1.05) cm, and those of the control group were (22.39±3.15) cm, (4.42±1.08) cm, and (4.02±1.21) cm, with statistically significant differences (t=11.239, 3.855, and 6.292, all P<0.001). The total effective rate of the experimental group was higher than that of the control group [93.75% (60/64) vs. 79.68% (51/64)], with a statistically significant difference (χ2=5.494, P=0.019). Conclusion Zhonggu granules combined with governor vessel moxibustion in the treatment of ankylosing spondylitis can effectively reduce the BASDAI and BASFI, alleviate the TCM symptoms, regulate the inflammatory polarization and bone metabolism indexes, and improve the physical examination indexes, proving to be a safe and effective treatment method.