Prostate is the most common gland for the three major diseases in men, such as chronic nonbacterial prostatitis (CNP), benign prostatic hyperplasia (BPH) and prostate cancer (PCa). However, there is lack of ideal biomarker for diagnosis with prostatic diseases. This prospective study quantified extracellular superoxide dismutase (SOD3) levels in serum or expressed prostatic secretion (EPS) with CNP, and in the prostatic tissues with BPH or PCa, to evaluate SOD3 as possible surrogate markers for diagnosis and treatment efficacy. The diagnostic ability of SOD3 with CNP was estimated by ROC analysis. The potential function of SOD3 in prostatic disoders was further investigated via bioinformatic analysis. As a result, SOD3 was significantly increased in CNP and BPH, but dereased in PCa compared to controls. SOD3 was significantly elevated in patients with CNP III (6.491643 ± 1.592292, P༜0.001), CNP IV (8.617879 ± 1.535176, P༜0.001) compared to normal controls (4.705892 ± 1.484917), discriminating CNP versus normal controls (accuracy = 0.831, 95%CI: 0.726–0.937, P༜0.001), CNP III versus CNP IV (accuracy = 0.868, 95%CI: 0.716–0.940, P༜0.001). Furthermore, SOD3 in serum were associated with clinical characteristics of patients with CNP including plevic pain, blood pressure and lecithin/leukocyte in EPS. Functionally, SOD3 mainly interacted with CP, DSG2, RBP4, and CFP via spercific amino acid residue, and participated in the signal pathway of superoxide radicals degradation and apoptotic execution phase. Our findings suggested that SOD3 and its interactors might play an important role in prostatic diseases, and SOD3 could be an ideal diagnostic marker and therapeutic target for CNP.