This paper proposes a high precision satellite beam agility control system that accounts for the satellite-ground time delay error caused by the rotation of the Earth. It is aimed to achieve high precision beam hopping of the phased array with sub-millisecond time granularity between multiple ground terminals in satellite communication. This system integrates a highly stable clock with a global navigation system to optimally calculate the satellite-ground transmission delay, correcting the orbital position through a two-iteration process. Simulation results show that the method can further improve the estimation accuracy of the satellite ground signal transmission delay under the satellite computationally constrained conditions. It achieves high time synchronization of the satellite-ground communication beam time and improves the efficiency of satellite-ground communication.