Abstract: Hydrogen fuel cell vehicles (HFCV) have zero pollution to the environment and have a long cruising range. At the same time, hydrogen fuel sources are very rich. Now HFCV is an important development direction for new energy vehicles. Air compressor is an important part of fuel cell. The centrifugal turbo compressor uses a high-speed permanent magnet motor to directly drive the turbine without speed-increasing gears and lubricating oil. A high speed permanent magnet motor controller is designed for hydrogen fuel cell air compressor. The sliding mode observer (SMO) is used to estimate the position and speed of the rotor, the motor controller adopts three-stage starting mode. A dual-core chip with integrated motor control processor’s is used in the controller with single current sensor and common IGBT power devices. The high speed motor controller is produced and the experimental platform is built, then the starting performance and speed regulation performance of the motor controller are tested. The controller has a simple structure with low cost and stable performance.