Gear transmission systems are widely used in various fields. The occurrence of gear cracks, tooth pitting, and other faults will lead to the dynamic characteristics deterioration of the transmission system. In order to calculate the meshing stiffness of faulty gear pairs more effectively and precisely, this article improves the loaded tooth contact analysis (LTCA) method by analyzing the influence of different fault types on gear deformation, including bending-shearing deformation and contact deformation, which combines the accuracy of the finite element method (FEM) and the rapidity of the analytical method (AM). The improved LTCA method can model the fault areas accurately and optimize the deformation coordination equation under the actual meshing situation of the faulty gear tooth, making it suitable for calculating the meshing stiffness of faulty gears. Based on the calculation results of the finite element method, the accuracy of the improved meshing stiffness calculation method has been verified, and the sensitivity of different fault type parameters on meshing stiffness has been studied.