Objective To systematically evaluate the efficacy and safety of single-port thoracoscopic surgery (SPTS) in the treatment of spontaneous pneumothorax. Methods Computer searches were conducted in PubMed, The Cochrane Library, Web of Science, Embase, CNKI, WanFang, and the Chinese Medical Association databases to collect randomized controlled trials (RCTs) and cohort studies on the comparison of efficacy and safety of SPTS and three-port thoracoscopic surgery (TPTS) for the treatment of spontaneous pneumothorax from their inception to March 2024. The Cochrane RCT bias risk assessment tool and the Newcastle-Ottawa Scale (NOS) were used to assess the quality of RCTs and cohort studies, respectively. Meta-analysis was performed using RevMan 5.4.1. Results A total of 68 studies were included, comprising 23 RCTs and 45 cohort studies with a total of 5403 patients. The NOS scores of the cohort studies were 7-8 points. Meta-analysis results showed that compared with TPTS, SPTS had less intraoperative blood loss [SMD=−1.58, 95%CI (−1.93, −1.22), P<0.001], shorter postoperative hospital stay [SMD=−1.05, 95%CI (−1.29, −0.82), P<0.001], shorter postoperative drainage tube placement time [SMD=−0.75, 95%CI (−1.00, −0.50), P<0.001], fewer postoperative complications [OR=0.34, 95%CI (0.26, 0.45), P<0.001], fewer postoperative recurrences [OR=0.48, 95%CI (0.32, 0.72), P<0.001], and less pain at 24, 48, and 72 h postoperatively [SMD=−1.71, 95%CI (−2.13, −1.30), P<0.001; SMD=−1.70, 95%CI (−2.35, −1.06), P<0.001; SMD=−1.72, 95%CI (−2.16, −1.29), P<0.001]. Conclusion SPTS is safe and effective in the treatment of spontaneous pneumothorax with high clinical value and can be further promoted in clinical practice. Considering the limitations in the number and quality of included studies, researches with larger sample sizes and higher quality are needed to validate the above conclusions.