The objective of this investigation was to explore the diagnostic capability of Prostate Specific Antigen Mass Ratio (PSAMR) combined with Prostate Imaging Reporting and Data System (PI-RADS) scoring for clinically significant prostate cancer (CSPC), develop and validate a Nomogram prediction model for the probability of prostate cancer occurrence in patients who have not undergone prostate biopsy. Initially, we retrospectively collected clinical and pathological data of patients who underwent trans-perineal prostate puncture at Yijishan Hospital of Wanan Medical College from July 2021 to January 2023. Through logistic univariate and multivariate regression analysis, independent risk factors for CSPC were determined. Receiver Operating Characteristic (ROC) curves were generated to compare the ability of different factors for diagnosis of CSPC. Then, we split the dataset into a training set and validation set, compared their heterogeneity, and developed a Nomogram prediction model based on the training set. Finally, we validated the Nomogram prediction model in terms of discrimination, calibration, and clinical usefulness. Logistic multivariate regression analysis illustrated that age [64-69 (OR = 2.736, P = 0.029); 69-75 (OR = 4.728, P = 0.001); > 75 (OR = 11.344, P < 0.001)], PSAMR [0.44-0.73 (OR = 4.144, P = 0.028); 0.73-1.64(OR = 13.022, P < 0.001); > 1.64(OR = 50.541, P < 0.001)], and PI-RADS score [4 points (OR = 7.780, P < 0.001); 5 points (OR = 24.533, P < 0.001)] were independent risk factors for CSPC. The Area Under the Curve (AUC) of the ROC curves of PSA, PSAMR, PI-RADS score, and PSAMR combined with PI-RADS score were respectively 0.797, 0.874, 0.889, and 0.928. The performance of PSAMR and PI-RADS score for diagnosis of CSPC was superior to PSA, but inferior to PSAMR combined with PI-RADS. Age, PSAMR, and PI-RADS were included in the Nomogram prediction model. The AUCs of the training set ROC curve and the validation set ROC curve were 0.943 (95% CI 0.917-0.970) and 0.878 (95% CI 0.816-0.940), respectively, in the discrimination validation. The calibration curve showed good consistency, and the decision analysis curve suggested the model had good clinical efficacy. We found that PSAMR combined with PI-RADS scoring had a strong diagnostic capability for CSPC, and provided a Nomogram prediction model to predict the probability of prostate cancer occurrence combined with clinical data.