Due to the tight installation space, strict weight requirements, numerous functional units and dense wireless equipments of small-size spacecraft, the traditional electronic system design of aircraft cannot meet the requirements of miniaturization and lightweight for small-size spacecraft. In this paper, a highly integrated electronic system suitable for small-size spacecraft is designed, in which many key technologies such as miniaturization and lightweight design technology, multi frequency wireless electromagnetic compatibility design technology, small aircraft low delay cooperative networking and high-precision differential positioning are adopted. The proposed highly integrated electronic system makes timing control, attitude and orbit control, wireless telemetry, networking communication, satellite navigation, power distribution and other functions integrated. The total weight of the system is about 7.62kg, which is much lighter than existing electronic system. The experiment results that the highly integrated electronic system achieves good effect. This technology has broad application prospects in small-size aircraft with strict weight and space requirements.