To estimate the failure probability of the photomultiplier tubes (PMT) underwater explosion test system, a method using information from fault tree analysis and uncertainty of data is presented. Based on the fuzzy set method and possibility theory, fuzzy fault tree method is a mathematical approach to model inaccuracy and uncertainty of the failure. The proposed model is able to quantify the fault tree of PMT explosion protection experiment system. In order to effectively investigate basic event failure probabilities without crisp quantitative historical failure data, fuzzy logic theory combined with expert judgement method is employed. The failure probability of the top event and the importance measures of basic events is also illustrated. The result demonstrates that the approach is apposite for the assessment of system failure. The research results can help professionals to decide whether and where to take preventive or corrective actions and help improve the underwater explosion-proof performance of PMT protective cover and fault diagnosis of test system.