The intermittent hole-digging tree-planting machine shows a periodic short-time peak load law in planting operation, and the operation process is “idling” for small loads most of the time, leading to large torque fluctuations in the transmission system, unscientific power matching, and high energy consumption. To solve the above problems, this article proposes to use a series of energy-saving flywheels in the transmission system of the tree planting machine. On the premise of obtaining holes that meet the target young tree planting requirements, the optimal power compensation strategy for the flywheel system of the tree planting machine is studied to reduce torque fluctuations in the power transmission system, use smaller power drive units, and save energy. Firstly, the nonlinear multi-body dynamics simulation model of soil cutting by the hole-digging component is established. The boundary and contact conditions are set to simulate the power consumption of the hole-digging component at three rotating speeds. Based on the simulation results, the flywheel power compensation strategy is discussed, and the torque fluctuation of the flywheel balance system is analyzed. The results showed that the higher the speed, the greater the power consumption. The power value suddenly increased from 17.82 kW (1.28 s) to 27.93 kW (1.43 s) when the speed was 220 r/min. Then, the power value rapidly decreased, and the power consumption presented a short-term peak feature. The transmission system’s maximum input power is determined as 17.82 kW according to the various simulated power consumption characteristics. The part exceeding the power consumption is compensated by the energy storage flywheel. The total compensation energy was 2382.5 J. After the flywheel system was involved, the maximum output power of the tractor power output shaft decreased by 36.2%, and the peak torque decreased from 445.7 N·m to 285.1 N·m. The power consumption obtained from the field test and simulation was similar, but the energy required to overcome peak load was jointly provided by the flywheel and the engine. The actual input power of the power output shaft during the energy release period of the flywheel system was 18.51 kW when the rotating speed of the hole-digging component was 220 r/min, and the relative error with the simulation value was 2.43%. The measured actual speed reduction of the flywheel system was 8.9%. After installing an energy storage flywheel in the transmission system of the tree planting machine, the output power of the power unit can be stabilized. Tree planting machines can be equipped with smaller power units, which can reduce energy consumption and exhaust emissions.