Objective To systematically evaluate the efficacy and safety of video-assisted thoracoscopic surgery (VATS) with different numbers of ports in the treatment of spontaneous pneumothorax. Methods We conducted a comprehensive search of CNKI, PubMed, The Cochrane Library, Web of Science, EMbase, Wanfang Data, and the Chinese Medical Journal Full-text Database for clinical controlled trials on VATS with different port numbers for spontaneous pneumothorax, from their inception to March 2023. Two researchers independently screened the literature and assessed its quality.The Newcastle-Ottawa Scale (NOS) was used to assess the methodological quality of cohort and case-control studies, and the Cochrane risk-of-bias tool was used to evaluate randomized controlled trials (RCT). Meta-analysis was performed using RevMan 5.4.1 software. Results A total of 107 studies were included, comprising 35 RCT, 2 cohort studies, and 70 case-control studies. All cohort and case-control studies included in the analysis had NOS scores≥7. The meta-analysis revealed that compared to two-port VATS (2P-VATS) and three-port VATS (3P-VATS), single-port thoracoscopic surgery (SPTS) was associated with less intraoperative blood loss (SMD=–1.58, 95%CI: –1.93 to –1.22, P<0.001; and SMD=–1.59, 95%CI: –2.03 to –1.14, P<0.001, respectively), shorter postoperative hospital stay (SMD=–1.05, 95%CI: –1.29 to –0.82, P<0.001; and SMD=–1.08, 95%CI: –1.39 to –0.77, P<0.001), shorter duration of postoperative chest tube drainage (SMD=–0.75, 95%CI: –1.00 to –0.50, P<0.001; and SMD=–1.23, 95%CI: –1.72 to –0.75, P<0.001), fewer postoperative complications (OR=0.34, 95%CI: 0.26 to 0.45, P<0.001; and OR=0.47, 95%CI: 0.33 to 0.68, P<0.001), and lower pain scores at 24, 48, and 72 hours after surgery (P<0.05). The operative time for SPTS was shorter than that for 2P-VATS (SMD=–0.53, 95%CI: –0.90 to –0.16, P=0.005) but showed no significant difference compared to 3P-VATS (P=0.21). When comparing 2P-VATS with 3P-VATS, 2P-VATS demonstrated less intraoperative blood loss (SMD=–1.02, 95%CI: –1.81 to –0.22, P=0.01), shorter postoperative hospital stay (SMD=–0.59, 95%CI: –1.11 to –0.06, P=0.03), shorter duration of chest tube drainage (SMD=–0.46, 95%CI: –0.85 to –0.08, P=0.02), fewer postoperative complications (OR=0.36, 95%CI: 0.22 to 0.59, P<0.001), and lower pain scores at 24, 48, and 72 hours after surgery (P≤0.05). Conclusion Both SPTS and 2P-VATS are effective and safe surgical options for spontaneous pneumothorax, deserving further promotion and application in clinical practice. However, due to limitations in the quantity and quality of the included studies, more large-sample, high-quality research is needed to validate these findings.