【Objective】 To identify the best surgical treatment for patients with calculous pyonephrosis by evaluating the clinical effectiveness of percutaneous nephrolithotripsy (PCNL) in stageⅠ, percutaneous nephrostomy (PCN) in stageⅠ, and percutaneous nephrolithotripsy in stageⅡ. 【Methods】 For publications published between Jan.2012 and Oct.2022, we thoroughly examined the databases of PubMed, Cochrane Library, Web of Science, EMBASE, CNKI, Wanfang, and VIP.We then chosed the literature based on the inclusion and exclusion criteria.After data were retrieved and literature quality was assessed, Review Manager software (RevMan 5.4.3, Cochrane Collaboration, Oxford, UK) was utilized to Meta-analysis. 【Results】 Out of 688 participants across 105 researches, we chosed 11 trials.Among them, 341 patients received both stageⅠPCN and stage ⅡPCNL (hereinafter referred to as phase ⅡPCNL), while 347 patients received stageⅠPCNL.According to the results of the Meta-analysis, there was no discernible difference between stage Ⅰ PCNL and stage Ⅱ PCNL in terms of stone clearance rate (P=0.95), operation duration (P=0.48), postoperative septic shock (P=0.36), or perirenal effusion infection (P=0.27).There were significant differences between stage Ⅰ PCNL and stage Ⅱ PCNL in fever (P=0.03), indwelling nephrostomy tube time (P=0.01), hospitalization costs (P=0.01), hospitalization time (P=0.01), and postoperative hospitalization time (P=0.02).The following two regimens were comparable in terms of stone clearance rate, operating time, postoperative perirenal effusion infection, and septic shock for patients with calculous pyonephrosis.Despite the fact that there were more patients who developed fever after stage ⅠPCNL, hospitalization costs were lower, indwelling nephrostomy tube time, overall hospitalization time, and postoperative hospitalization time were all reduced. 【Conclusion】 ⅠPCNL was affordable, safe, and successful for treating renal and upper ureteral calculi with pyonephrosis, and it had some promotional value in clinical practice.