Risk assessment of deep shale reservoirs is very important for subsurface energy development. However, due to complex geological environments and physicochemical interactions, shale reservoir fabric parameters exhibit variability. Moreover, the actual investigation and testing information is very limited, which is a typical small-sample problem. In this paper, the heterogeneity and statistical characteristics of deep shale reservoirs are clarified by the measured mechanical parameters. A deep learning method for deep shale reservoirs with limited survey data information is proposed. The variability of deep shale reservoirs is characterized by random field theory. A variable stiffness method and stochastic analysis method are developed to evaluate the risk of deep shale reservoirs. The detailed workflow of the stochastic risk assessment framework is presented. The frequency distribution and failure risk of deep shale reservoirs are calculated and analyzed. The risk assessment of deep shale reservoirs under different model parameters is discussed. The results show that a stochastic risk assessment framework of deep shale reservoirs, using a deep learning method and random field theory, is scientifically reasonable. The scatter plots of the elasticity modulus (EM), cohesive force (CF), and Poisson ratio (PR) distribute along the 45-degree line. The different distributed variables of EM, CF, and PR have a positive correlation. The statistical properties of the measurement data and deep learning data are approximately the same. The principal stress of deep shale follows the normal distribution with significance level 0.1. Under positive copula conditions, the maximum failure probability is 5.99%. Under negative copula conditions, the maximum failure probability is 4.58%. Different copula functions under positive and negative copula conditions have different failure probabilities. For the exponential correlation structure, the minimum failure probability is 3.46%, while the maximum failure probability is 6.19%. The mean failure probability of the EM, CF, and PR of deep shale reservoirs is 4.85%. Different random field-related structures and parameters have different influences on the failure risk.