Objective To systematically evaluate the efficacy and complications of soft ureteroscopic lithotripsy (SUL) and percutaneous nephrolithotomy (PCNL) in the treatment of urinary calculi and to provide evidence-proof medicine basis for the popularization and application of flexible ureteroscopic lithotripsy. Methods PubMed, EMBASE, ScienceDirect, Cochrane Library, China knowledge Network Database (CNKI), China VIP Database, Wanfang Database, and China Biomedical Literature Database (CBM) were searched for randomized controlled trials (RCT) related to soft ureteroscopic lithotripsy and percutaneous nephrolithotomy in the treatment of urinary calculi from Jan. 2010 to Mar. 2022. The bias risk of each included literature was assessed according to the standard of Cochrane manual 5.1.0. The collected data were meta-analyzed by RevMan 5.4 statistical software. Results Ultimately, 6 RCT (a total of 794 samples) were included for meta-analysis. Heterogeneity test results of stone clearance rate were chi2 = 2.44, df = 5, P = 0.79 > 0.05, and I2 = 0%, indicating none obvious heterogeneity among the included research data. The test of WMD was Z = 2.11 (P = 0.03). It could be considered that compared with PCNL in the treatment of urinary calculi, SUL had a higher stone clearance rate in patients with urolithiasis. Secondly, heterogeneity test of operation time was chi2 = 184.95, df = 5, P < 0.00001, and I2 = 97%. The results of heterogeneity test of intraoperative blood loss displayed chi2 = 645.47, df = 5, P < 0.00001, and I2 = 99%. Then, heterogeneity test results of postoperative hospital stay existed chi2 = 57.37, df = 5, P < 0.00001, and I2 = 91% with an obvious heterogeneity. According to the results of this analysis, it could be considered that compared with PCNL in the treatment of urolithiasis, the operation time of SUL in the treatment of urolithiasis was longer, but the amount of intraoperative bleeding and postoperative hospital stay was significantly reduced. The results of heterogeneity of stress index level NE showed as chi2 = 0.32, df = 2, P = 0.85 > 0.05, and I2 = 0%, and COR was chi2 = 1.09, df = 1, P = 0.30 > 0.05, and I2 = 8%. It showed that there was no obvious heterogeneity. The heterogeneity of ACTH was chi2 = 390.36, df = 2, P < 0.00001, and I2 = 99%, suggesting obvious heterogeneity. The test of combined effect dose WMD was Z = 21.90, 4.50, and 15.42, (P < 0.00001). It could be considered that there was a statistical difference in the WMD of stress response between patients with urinary calculi treated by soft ureteroscope and percutaneous nephrolithotomy, indicating that the stress response of patients with urinary calculi treated with SUL is less than that of PCNL. For the heterogeneity test of serum creatinine level, NE showed chi2 = 0.78, df = 2, P = 0.68 > 0.05, and I2 = 0% without obvious heterogeneity, and the combined effect dose WMD is analyzed by random effect model. The test of combined effect dose WMD was Z = 4.22 (P < 0.00001). It can be considered that the improvement of serum creatinine level in patients with urolithiasis treated with SUL was better than that of PCNL. The results of heterogeneity test on the safety of operation are as follows: chi2 = 13.76, df = 5, P = 0.02, and I2 = 64%, indicating obvious heterogeneity among the included research data. The combined effect dose of WMD was Z = 5.53 (P < 0.00001). This could be considered that soft ureteroscopic lithotripsy had higher safety and less postoperative complications than percutaneous nephrolithotomy in the treatment of urinary calculi. An inverted funnel chart was used to analyze the publication bias of the study with stone clearance rate as the outcome index. The results showed that the figure was not completely symmetrical and the Egger's test showed that the figure was P = 0.0005 < 0.001. It was suggested that there may be a certain degree of publication bias. Conclusion PCNL and SUL can achieve higher stone clearance rate in the treatment of renal calculi. However, SUL has the advantages of less intraoperative bleeding, short stress reaction and postoperative hospital stay, less damage to renal function, and low incidence of complications, which is beneficial to the rapid recovery of patients after operation. More studies with higher methodological quality and longer intervention time are needed to further verify.