Many uncertain factors, e.g. surrounding rock physical and mechanical characteristics, are important influence effecting on lining structure safety. By comprehensively considering uncertainties of surrounding rock conditions (lining structure and initial stress), we put forward a new method used to quantitative analysis on the lining structure safety. Analyzing the uncertainties and their distribution characteristics of hydraulic tunnels, we adopted stochastic finite elements method to calculate failure probability of lining structures corresponding to various geological conditions, and then the reliability and sensitivity were achieved. Applying the presented method to a practical project, we got the failure probability of the tunnel lining structure under the construction condition, which provided great support for structure optimal design and tunnel construction safety protection.