Abstract The most common site of metastasis of prostate cancer (PCa) is bone. Skeletal-related events can increase the risk of death in patients with PCa by 28%. Due to the low detection rate of lesions in patients with low prostate-specific antigen (PSA) levels, the value of 99m Tc methylene diphosphonate ( 99m Tc-MDP) bone scintigraphy is limited. Prostate-specific membrane antigen (PSMA) is a small molecular probe that can efficiently and specifically detect PCa lesions. This prospective study aimed to evaluate the difference between 99m Tc-PSMA single-photon emission computed tomography (SPECT)/CT and 99m Tc-MDP SPECT/CT in the detection of bone metastasis in PCa. A total of 74 men with pathologically confirmed PCa from October 2019 to November 2021 were prospectively enrolled in this study. The median age was 70 (range, 55–87) years. All patients underwent both 99m Tc-PSMA SPECT/CT and 99m Tc-MDP SPECT/CT at an average interval of 12.1 (range, 1–14) days. The detected imaging-positive bone lesions were scored as “typical metastasis” or “equivocal metastasis” by a standard reporting schema. Subsequent therapy modality details were observed through follow-up. Twenty-five of the 74 patients were diagnosed with bone metastases. 99m Tc-PSMA SPECT/CT and 99m Tc-MDP SPECT/CT detected 20 and 18 bone metastases, with sensitivities of 80.0% (20/25) and 72.0% (18/25), specificities of 100.0% (49/49) and 81.3% (40/49), and AUCs of 88.0% and 84.9%, respectively. There was a significant difference in the AUC between the two imaging methods ( P  < 0.001). In an analysis of the number of bone metastasis lesions, the proportion of “typical metastasis” versus “equivocal metastasis” detected by the two imaging methods was 26.3:1 (PSMA) and 2.9:1 (MDP), and the difference was statistically significant ( P  = 0.005). There was a significant difference in the detection of bone metastatic lesions by 99m Tc-PSMA and 99m Tc-MDP when the maximum diameter of the lesions was ≤ 0.6 cm ( P  < 0.05). The optimal cut-off value for PSA was 2.635 ng/mL (PSMA) and 15.275 ng/mL (MDP). 99m Tc-PSMA SPECT/CT led to a change in management to a more individualized therapy modality for 11 of 74 men (14.9%). 99m Tc-PSMA SPECT/CT was superior to 99m Tc-MDP SPECT/CT in the detection of bone metastases in PCa, especially for small lesions and in patients with low PSA levels, and demonstrated an additional benefit of providing information on extraskeletal metastases. With regard to therapy, 99m Tc-PSMA scans might have utility in improving the subsequent therapy modality.