Brake by wire that allows a number of braking functions exists on commercial vehicles under the name electronic pneumatic braking system, which can improve braking comfort and safety of commercial vehicle. The design of braking force distribution control method has drawn much more attention. Considering structure characteristics of electronic pneumatic braking system, a control method with a three-layer hierarchical structure is proposed. The first layer presents an estimation method towards vehicle mass and centre of gravity combining Kalman filter with recursive least square. The second layer is developed by designing a fixed relationship between the brake pedal displacement and vehicle braking deceleration. A deceleration control method that only uses brake pedal displacement as input is applied to make the vehicle follow the desired deceleration. The third layer includes a braking force distribution control method between the front and rear axles. The vehicle deceleration can be achieved with a smooth axle load transfer process based on linear matrix inequality. In addition, the controllers of wheel slip rate and valve hysteresis compensation are designed to improve control accuracy and efficiency. Utilizing a hardware-in-the-loop simulation test rig of electronic pneumatic braking system, the experiment results show that the control method can improve the braking performance of vehicle.