Design a brushless direct current motor control system basing on STM32F103RB as the main control chip. Through output PWM to the MC33035 chip and the pressure differential feedback, so as to achieve the purpose of stable inside and outside differential pressure of negative pressure compartment.Use STM32 internal timer and hardware multiplier to complete the generation of PWM signal. Realize double closedloop incremental PI control by pressure difference and current.At the same time control system is described in detail. It can be seen from the test results，The maximum in capsule pressure is -60 Pa and the minimum is -120 Pa during entire air transport process. The security numerical is -15 Pa. The negative pressure is proportional to the height in the flight.This control system has a good dynamic performance,and the control precision reaches advanced level in China.