Background To study the effectiveness and safety of aqueous humor PCR viral detection in the diagnosis of PSS. Methods 20 patients (case group) with PSS who suffered from recurrences and poor intraocular pressure (IOP) control by use of drugs underwent anterior chamber puncture. The concentration of different viruses in aqueous humor were detected by PCR. 20 patients (control group) with POAG were given the same treatment and we compared the difference of positive rate of the viruses between two groups. Finally, the effectiveness and safety of aqueous humor PCR viral detection in the diagnosis of PSS were observed. Besides, the advantage of PCR viral detection technology in treatment was evaluated. Results No complications and long-term sequelae related to anterior chamber puncture were found. The total positive rate of aqueous humor viral detection was 30% (6/20) in case group ,and was found none in control group (0/20) (P = 0.027). Then, we divided the case group into two groups. Six virus positive patients were given local and systemic antiviral treatment for 3 months and then interrupted the treatment. Fourteen patients left were given no antiviral treatment. All PSS patients were observed for 9 months from the first time of treatment. There is significant difference between two groups in recurrence rate (P = 0.013). Conclusions Viral infection is a risk factor of PSS. The detection of virus in aqueous humor by PCR is effective and safe for diagnosis of PSS, and helpful for targeted treatment on virus-positive patients.