In the lunar exploration CubeSat mission, the complex space environment and limited onboard resources place higher requirements on the anti-radiation design of the integrated electronic system. By analyzing the destructive effects of the deep space radiation environment and the failure mechanism of components, a hardening scheme for the integrated electronic system of lunar exploration CubeSat is proposed. A variety of measures are taken to target the key components and circuit parts in the integrated electronic system that are susceptible to radiation damage. A prototype verification system for anti-radiation hardening technology was designed and system-level testing was carried out. Research results show that adopting effective radiation-resistant hardening technology can significantly improve the safety and reliability of CubeSat integrated electronic systems in deep space environments.