The Institute of Modern Physics (IMP), Chinese Academy of Sciences (CAS) has recently initiated the development of an electrostatic high-voltage ion accelerator. As the core component of this accelerator type, the high-voltage generator is required to meet design specifications including a maximum operational voltage of 4.2 MV, voltage instability below ±0.1%, and a ripple coefficient within ±0.1%. To achieve these parameters, a simulation-based modeling approach was first implemented for the overall structural design and optimization of the high-voltage generator, thereby enhancing operational safety and stability. For the critical high-frequency transformer subsystem within the generator, a field-circuit coupling methodology was employed to analyze and optimize both its circuit topology and electrical parameters. Concurrently, thermal dissipation structure modifications were implemented to ensure stable output performance of the transformer. Furthermore, a high-precision voltage stabilization scheme was developed for the generator’s control system and optimized control strategies was proposed to enhance operational reliability.The research demonstrates that the proposed high-voltage generator design meets the specified technical requirements of the project. This systematic approach integrating electromagnetic design, thermal management optimization, and advanced control methodologies provides valuable insights for developing next-generation high-voltage power systems in accelerator applications.