This study aimed to identify predictors of renal function improvement (RFI) after percutaneous nephrolithotomy (PCNL) in chronic kidney disease (CKD) patients with complex kidney stones, and to develop a predictive nomogram. A retrospective analysis was conducted on 107 enrolled patients from January 2021 to December 2024. Among the 107 enrolled patients (male-to-female ratio 2.57:1), the mean age was 58.1 ± 9.5 years. Twenty-seven point one percent exhibited RFI. Multivariable analysis revealed that higher preoperative hemoglobin (OR 1.051, 95% CI 1.021–1.038, p = 0.001), lower baseline estimated glomerular filtration rate (eGFR) (OR 0.854, 95% CI 0.789–0.924, p < 0.001), and absence of urinary tract infection (UTI) (OR 0.331, 95% CI 0.119–0.925, p = 0.035) were independently associated with RFI. Based on these parameters, a nomogram was developed. This model demonstrated a predictive accuracy of 77.9%. After bootstrapping, the calibration curve showed a mean absolute error (MAE) of 0.079. Decision curve analysis (DCA) confirmed its clinical utility across a wide probability threshold (15–94%). In summary, a nomogram based on preoperative hemoglobin, eGFR, and UTI status can help predict RFI after PCNL. Managing anemia and infection before surgery is crucial to improving outcomes in these high-risk patients.