Enhanced geothermal system (EGS) is the main means of exploiting hot dry rock (HDR) geothermal resources. The utilization of liquid nitrogen is expected to solve the difficulties of conventional fracturing means in terms of high fracture pressure and single fracture formation. Computational techniques can contribute to confirming the effect of liquid nitrogen on the deterioration of the mechanical properties of granite. In this study, the process of liquid nitrogen cooling is numerically simulated with the granite matrix being reconstructed using the quartet structure generation set. After liquid nitrogen cooling, the crack distribution of granite under loading process is analyzed by percolation model, where the depth-first search algorithm is used. The results show that the increases in initial temperature, heat transfer coefficients, and the heterogeneity of the coefficient of thermal expansion promote greater thermal stress during liquid nitrogen cooling. The heterogeneity in particular has a significant impact on the complexity of stress distribution. Further, during loading process, greater crack density is generated in granite after liquid nitrogen treatment.