Today，the controller of most portable AUV is designed based on X86 architecture processor. It has a large volume，low integration，high power consumption. Based on the requirements of AUV control system，the controller of the portable AUV was designed which chooses I.MX6Q CPU of ARM Cortex-A9 series as the hardware core, chooses circuit which integrates power supply，GPIO，serial port expansion，net extension，AD sampling，and CAN interface modules into an organic whole as the hardware platform and chooses the embedded Linux operation system as software running environment. The controller is designed customized on the hardware and the Linux device driver of each module is designed or transplanted on the software. By the test results show that this controller can not only solve the problem of AUV electronic cabin occupies large volume，low level of integration，and high power consumption effectively，but also the modules has reliable performance. It makes a good foundation for portable AUV to realize the productization.