Our purpose was to compare the performance of prostate-specific membrane antigen (PSMA)-positron emission tomography (PET) traditional fixed threshold (FT) and newly established Prostate Imaging Reporting and Data System (PI-RADS)-based segmented threshold (ST) for diagnosing clinically significant prostate cancer (csPCa). The study retrospectively included 218 patients who underwent multiparametric magnetic resonance imaging (mpMRI) and PSMA-PET examination for suspected prostate cancer (PCa) from January 2018 to November 2021. Lesions with Gleason score ≥ 3 + 4 were diagnosed as csPCa. In PSMA-PET maximum standardized uptake value (SUVmax), the FT for all the lesions and STs for lesions with different PI-RADS score for diagnosing csPCa were determined by receiver operating characteristic (ROC) curves analysis and compared with Z test. The McNemar test was used to compare sensitivity and specificity. Among the 218 patients, there were 113 csPCa and 105 non-csPCa. The PSMA-PET FT was SUVmax > 5.3 (area under the curve, AUC = 0.842) and STs for PI-RADS 3/4/5 were SUVmax > 4.2/5.7/6.0 (AUCs = 0.870/0.867/0.882), respectively. The AUC of PSMA-PET ST was higher than that of PSMA-PET FT (0.872 vs. 0.842), especially for PI-RADS 3 (0.870 vs. 0.653). Multimodality diagnostic criteria combining PSMA-PET ST and PI-RADS scores of mpMRI was established and its AUC was higher than that of PSMA-PET ST (0.893 vs. 0.872) and significantly higher than that of PSMA-PET FT (0.893 vs. 0.842) with an improvement in sensitivity (93% vs. 78%, p < 0.05) without significantly sacrificing specificity (86% vs. 91%, p > 0.05). For diagnosing csPCa, PI-RADS-based PSMA-PET segmented threshold achieved better performance than traditional fixed threshold, especially for PI-RADS 3 lesions. Multimodality diagnostic criteria demonstrated higher diagnostic performance than segmented threshold and significantly better than PSMA-PET fixed threshold for detecting csPCa.