Objective To evaluate the diagnostic value of magnetic resonance spectroscopy analysis in patients with prostate specific antigen (PSA) abnormal prostate disease. Methods The patients who had abnormal PSA from January 2017 to December 2018 in Weifang People′s Hospital were selected. Patients with prostate puncture indications were as research target. A total of 137 patients including 44 patients with prostate cancer and 93 patients with benign prostatic hyperplasia were diagnosed by puncture. All patients underwent magnetic resonance scan and enhancement and spectroscopy before surgery. The comparative value of magnetic resonance scan + enhancement, magnetic resonance spectroscopy and joint examination was obtained. Results Sensitivity of magnetic resonance imaging and enhancement was 77.3% (34/44), specificity was 86.0% (80/93), and accuracy was 83.2% (114/137). Sensitivity of magnetic resonance spectroscopy was 52.3% (23/44), specificity was 77.4% (72/93), and accuracy was 69.3% (95/137). The sensitivity of the combined application was 90.9% (40/44), specificity was 91.4% (85/93), and accuracy was 91.2% (125/137). Conclusions The application of magnetic resonance spectroscopy can increase the sensitivity, specificity and accuracy of magnetic resonance plain scan and intensive examination for diagnosis of prostate cancer.