Gearbox fault diagnosis based on vibration sensing has drawn much attention for a long time. For highly integrated complicated mechanical systems, the intercoupling of structure transfer paths results in a great reduction or even change of signal characteristics during the process of original vibration transmission. Therefore, using gearbox housing vibration signal to identify gear meshing excitation signal is of great significance to eliminate the influence of structure transfer paths, but accompanied by huge scientific challenges. This paper establishes an analytical mathematical description of the whole transfer process from gear meshing excitation to housing vibration. The gear meshing stiffness (GMS) identification approach is proposed by using housing vibration signals for two stages of inversion based on the mathematical description. Specifically, the linear system equations of transfer path analysis are first inverted to identify the bearing dynamic forces. Then the dynamic differential equations are inverted to identify the GMS. Numerical simulation and experimental results demonstrate the proposed method can realize gear fault diagnosis better than the original housing vibration signal and has the potential to be generalized to other speeds and loads. Some interesting properties are discovered in the identified GMS spectra, and the results also validate the rationality of using meshing stiffness to describe the actual gear meshing process. The identified GMS has a clear physical meaning and is thus very useful for fault diagnosis of the complicated equipment.