In order to meet the needs of flight height information of a small unmanned aerial vehicle (UAV), designing a kind of detecting system adopting the MEMS height pressure sensor and it is used to obtain the relative height of UAV. It uses the outside ambient temperature to compensate the error of relative height at the same time. The system adopts a MS5611 digital atmospheric pressure sensor to obtain pressure value and temperature value of the outside world, and adopts the microprocessor STM32F103 to deal with the related data and control detecting system. Besides, Elaborating the theory of detecting barometric altitude, the design scheme of hardware circuit and software algorithm of the detecting system. Finally, the experimental data show that this design scheme can meet the needs of UAV for height measurement.