Objective To evaluate the effects of spinal manipulation therapy (SMT) on chronic nonspecific neck pain (CNSNP) by using World Health Organization Family International Classifications (WHO-FICs). Methods Randomized controlled trials (RCTs) about the effects of SMT on CNSNP were searched from PubMed, Web of Science, Cochrane Library, EMBASE, EBSCO, CBM and CNKI from database establishment to December 31st, 2021. At least two researchers extracted the data. Cochrane bias risk assessment tool and Physiotherapy Evidence Database Scale were used to evaluate the quality of the included articles. Revman 5.4 software and Stata 16.0 software were used for meta-analyses and publication bias analysis respectively. Results A total of 15 RCTs that represented 1 067 participants were evaluated. In terms of body functions, compared with the control group, SMT significantly reduced Visual Analog Score for pain (MD = -0.85, 95%CI -1.06 to -0.63, P < 0.00001) and Numerical Rating Scale (MD = -0.92, 95%CI -1.29 to -0.55, P < 0.001), increased pressure pain thresholds (SMD = 0.67, 95%CI 0.47 to 0.86, P < 0.001), cervical range of motion (ROM) of flexion/extension (SMD = 0.51, 95%CI 0.33 to 0.68, P < 0.001) and rotation (SMD = 0.20, 95%CI 0.01 to 0.38, P = 0.04), improved root mean square of cervical muscles electromygraphy (MD = 2.17, 95%CI 0.06 to 4.29, P = 0.04), but not significantly in cervical ROM of lateral flexion (SMD = 0.19, 95%CI -0.00 to 0.38, P = 0.06), cervical strength (SMD = -0.18, 95%CI -0.84 to 0.49, P = 0.60) and endurance (SMD = 0.18, 95%CI -0.39 to 0.75, P = 0.53). In term of activities and participation, SMT significantly improved cervical disability (MD = -0.96, 95%CI -1.55 to -0.38, P = 0.001), but not significantly in health status of patients with CNSNP (SMD = 0.08, 95%CI -0.03 to 0.20, P = 0.15). Conclusion SMT could improve pain intensity, pain sensitivity, cervical ROM and disability in patients with CNSNP, but its efficacy on muscle function, proprioception and health status is unclear.