Focusing on gear transmission systems having thin web and hole structures for energy saving and weight reduction, this work aims to propose an effective method for dynamical modeling and characteristics identification of spalling in lightweight gear systems. A novel three-dimensional (3D) spalling morphology modeling method is developed by the optical scanner. Subsequently, an analytical-finite element (AFE) model is established to calculate the mesh stiffness with weight reduction structures and spalled teeth. Additionally, the discrete tooth surfaces from coordinate measuring machines (CMMs) are used to calculate the no-load static transmission error (NLSTE). A rigid-flexible coupling dynamic model is introduced into the gear-rotor-bearing system considering the lightweight rotor and friction characteristics. The effects of spalling fault levels, the number and distribution form of spalled teeth on dynamic characteristics of the lightweight gear system are investigated. The numerical and experimental results demonstrate the existence of coupling modulation between spalling and holes, but it can still be identified by time and frequency domain characteristics. The proposed model and analysis results provide important references for identifying spalling in lightweight gear systems.