Objective To explore the clinical value of methylation at promoter sites of urine protein kinase Y-linked （PRKY） gene in the early diagnosis of prostate cancer（PCa）. Methods Urine samples were collected from 50 suspected PCa patients. After extracting DNA， the methylation levels of the PRKY gene promoter sites cg05163709， cg08045599， and cg05618150 were detected using quantitative methylation-specific PCR （qMSP）. Simultaneously， the patients were divided into the benign prostatic hyperplasia （BPH） group and the PCa group. The differences in clinical indicators between the two groups were analyzed， as well as the methylation status of the PRKY gene promoter sites in the urine of the two groups of patients. The receiver operating characteristic （ROC） curve of PRKY promoter sites methylation was established， and the area under the curve （AUC） was calculated to analyze the diagnostic value of PRKY promoter sites methylation in PCa， and to perform combined diagnosis with clinical indicators. Results The methylation rates of cg05163709 and cg05618150 in urine specimens of PCa patients were significantly higher than those of BPH patients. The AUC for cg05163709 methylation in diagnosing PCa was 0.762， with a sensitivity of 86.70%. It showed better performance in early screening for PCa compared to total prostate specific antigen （tPSA）， percentage free prostate specific antigen（f/tPSA）and prostate specific antigen density （PSAD）index. We found that the AUC for cg05618150 methylation in conjunction with PSAD in diagnosing PCa was 0.787， with a sensitivity of 86.70%. The AUC of cg05163709 methylation and PSAD in the joint diagnosis of PCa was 0.855， and the specificity could reach 95.00%. Conclusion The methylation of urine PRKY gene promoter sites cg05163709 and cg05618150 shows high sensitivity and specificity in diagnosing PCa， making them promising biomarkers for early detection of PCa.