The complex three-shaft three-reducer structural designs of helicopter transmission systems are prone to changes in the relative positions of shafting under the conditions of main rotor and tail rotor loads. These changes will affect the transmission characteristics of the entire transmission system. In this study, the planetary gear trains of helicopters were examined. Due to the fact that these structures are considered to be the most representative structures of the main reducers of helicopters, they were selected as the study objects for the purpose of examining the meshing characteristics of planetary gear trains when the relative positions of the shafting changed due to the position changes of the main rotor shafts under variable load conditions. It was found that by embedding the comprehensive time-varying meshing stiffness values of the main rotor shafts at different positions, a dynamic model of the relative position changes of the planetary gear trains could be established. Then, combined with the multibody dynamics software, the meshing characteristics of the sun gears, and the planetary gears, the planetary gears and the inner ring gears were simulated and analyzed under different inclinations and offsets of the shafting. The results obtained in this study revealed the following: (1) the average meshing force of the gears increased with the increases in the angle inclinations, and the meshing force between the sun gears and the planetary gears increased faster than the meshing force between the planetary gears and the inner ring gears. It was observed that during the changes in the shafting tilt positions, obvious side frequency signals had appeared around the peak of the meshing frequency in the spectrum. Then, with the continuous increases in the tilt position, the peak was gradually submerged; (2) the average meshing force of the gears increased with the increases in the offset, and the increasing trend of the meshing force between the sun gears and the planetary gears was similar to that observed between the planetary gears and the inner ring gears. It was found that when the shafting offset position changed, there were obvious first and second frequency doubling in the spectrum; (3) the mass center orbit radii of the sun gears increased with the increases in the shafting position changes, and the changes in the angular tilt position were found to have greater influencing effects on the mass center orbit radii of the sun gears than the changes in the offset positions. This study’s research findings will provide a theoretical basis for future operational status monitoring of the main transmission systems of helicopters and are of major significance for improvements in the operational stability of helicopter transmission systems, which will potentially ensure safe and efficient operations.