To accurately assess the effects of gear manufacturing deviations on gear system dynamics, advanced measurement techniques are employed to capture actual tooth surface deviations. These deviations are mapped to contact points on the gear meshing action plane through interpolation. Considering the superposition of contact point deviations between the driving and driven gears, along with differences in tooth surface deviations, a long-period loaded tooth contact analysis (LTCA) is conducted to obtain excitations of long-period time-varying mesh stiffness (TVMS) and comprehensive mesh error (CME) for dynamic analysis. Using Fast Fourier Transform (FFT) analysis, the gear meshing frequency, rotating frequency, and hunting tooth frequency are identified within these excitations. A dynamic model of the herringbone gear system is developed using the generalized finite element method. By incorporating these excitations into the dynamic model, the effects of actual tooth surface deviations on the system’s dynamic characteristics are analyzed. When accounting for actual tooth surface deviations, complex modulation phenomena appear in the system’s vibration spectrum, including modulation between hunting tooth frequency, meshing frequency, and rotating frequency. Finally, a power-closed herringbone gear vibration test bench is constructed, and vibration acceleration tests at the bearing seat are conducted to validate the effectiveness of the proposed dynamic model.