Chronic low back pain (CLBP) is a common health problem. Pilates is a unique exercise therapy. This meta-analysis aims to evaluate the efficacy of Pilates on pain, functional disorders, and quality of life in patients with chronic low back pain (CLBP). PubMed, Web of Science, CNKI, VIP, Wanfang Data, CBM, EBSCO, and Embase were searched. Randomized controlled trials of Pilates in the treatment of CLBP were collected based on the inclusion and exclusion criteria. The meta-analysis was performed using RevMan 5.4 and Stata 12.2. 19 randomized controlled trials with a total of 1108 patients were included. Compared with the controls, the results showed the following values: Pain Scale [standard mean difference; SMD = -1.31, 95%CI (-1.80, -0.83), p < 0.00001], Oswestry Disability Index (ODI) [mean difference; MD = -4.35, 95%CI (-5.77, -2.94), p < 0.00001], Roland-Morris Disability Questionnaire (RMDQ) [MD = -2.26, 95%CI (-4.45, -0.08), p = 0.04], 36-item Short-Form (SF-36) (Physical Function (PF) [MD = 5.09, 95%CI (0.20, 9.99), p = 0.04], Role Physical (RP) [MD = 5.02, 95%CI (-1.03, 11.06), p = 0.10], Bodily Pain (BP) [MD = 8.79, 95%CI (-1.57, 19.16), p = 0.10], General Health (GH) [MD = 8.45, 95%CI (-5.61, 22.51), p = 0.24], Vitality (VT) [MD = 8.20, 95%CI(-2.30, 18.71), p = 0.13], Social Functioning (SF) [MD = -1.11, 95%CI (-7.70, 5.48), p = 0.74], Role Emotional (RE) [MD = 0.86, 95%CI (-5.53, 7.25), p = 0.79], Mental Health (MH) [MD = 11.04, 95%CI (-12.51, 34.59), p = 0.36]), Quebec Back in Disability Scale (QBPDS) [MD = -5.51, 95%CI (-23.84, 12.81), p = 0.56], and the sit-and-reach test [MD = 1.81, 95%CI (-0.25, 3.88), p = 0.09]. This meta-analysis reveals that Pilates may have positive efficacy for pain relief and the improvement of functional disorders in CLBP patients, but the improvement in quality of life seems to be less obvious. PROSPERO CRD42022348173.