In order to achieve high-precision robust control of pneumatic cylinder motion trajectory, the mathematical model of proportional valve-controlled pneumatic cylinder system was established, and a non-linear deterministic robust controller was designed on the basis of the backstepping method, which can effectively suppress the effects of system model parameter uncertainty, unmodelled dynamics and external disturbances. The Simulink module in MATLAB was used to construct a simulation model of the pneumatic cylinder motion trajectory tracking control system. A real-time control system for pneumatic cylinder motion trajectory based on a non-linear deterministic robust controller was developed using xPC-Target in MATLAB/Simulink. The simulation results show that the designed controller is feasible. The test results show that the controller can effectively track the reference trajectory, with a maximum tracking error of 0.89 mm for a 0.3 Hz sinusoidal trajectory, which is about 2.97% of the amplitude, and 1.02 mm for a 0.4 Hz sinusoidal trajectory, which is 3.4% of the amplitude.