To examine the health-related quality of life (HRQoL) and factors associated with HRQoL in Chinese patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) using two generic preference-based HRQoL instruments, EQ-5D (plus EQ-VAS) and SF-6D, with the results compared with general population. CP/CPPS patients were recruited from two tertiary referral hospitals, and the general populations were randomly approached. After informed consent, subjects were interviewed using EQ-5D, EQ-VAS and SF-6D, and their socio-demographic and medical information was solicited. Compared to the general population (n = 364), CP/CPPS patients (n = 268) reported significantly worse HRQoL with median score of the EQ-5D utility index (0.73 vs. 0.85), SF-6D utility index (0.76 vs. 0.81), and EQ-VAS (70.0 vs. 85.0). Multiple linear regression analyses showed pain symptom had the strongest predictive power for HRQoL, compared to symptom duration and urinary symptom. Socio-demographic factors and comorbidities did not significantly contribute to poorer HRQoL. CP/CPPS patients experienced deteriorated HRQoL with lower health-related utility scores compared to general population, and pain severity was the main physical symptom predicting decreased health-related utility. Further studies are needed to provide the reference utility index for the comparison and better characterizing the influence of geographic and cultural factors on variation of health-related utility of CP/CPPS patients.