A precise control method of brake cylinder pressure based on backstepping was proposed for the heavy-haul train equipped with electronically controlled pneumatic (ECP) brake system. A control model of ECP brake system with strict feedback form was established through equivalent continuous processing and linearization. By introducing the uncertainties with known upper bound, and adopting the sliding mode variable structure with exponential approach law, the local robustness of the system was achieved. A control law based on backstepping was designed by constructing error variables and Lyapunov function. A first-order filter was introduced to solve the problem of counting the derivative repeatedly in the control law. The performance of the controller was analyzed through hardware-in-loop test. Test results showed that, comparing with the traditional controller, the controller of brake cylinder pressure based on backstepping had a higher control accuracy, and its steady state control error was within the range of ±8 kPa without obviously overshoot in the pressure regulation process. In addition, the introduction of dead zone in the controller can significantly reduce the operation times of the AV/RV valve and improve the service life of the system.