The invention discloses a robust neural network control system for a micro-electro-mechanical system (MEMS) gyroscope based on sliding mode compensation and a control method of the control system. The control system comprises a given trajectory generation module, a sliding mode surface definition module, a neural network controller, a weight adaptive mechanism module, a sliding mode compensator, an MEMS gyroscope system, a proportional-differential control module, a first adder and a second adder. The control method of the control system comprises the following steps of: establishing an MEMS gyroscope kinetic model based on a sliding mode surface, designing a controller structure, and designing an updating algorithm of a radial basis function (RBF) network weight, so that the trajectory of the MEMS gyroscope is tacked. By the control method, the influence of the unknown dynamic characteristic of the MEMS gyroscope and noise interference can be compensated on line, the vibration trajectory of the MEMS gyroscope completely follows a reference trajectory, and the anti-interference robustness and reliability of the system are improved; the updating algorithm of the network weight is designed on the basis of a Lyapunov stability theory, so that the stability of a closed-loop system is ensured; and a powerful basis is provided for expanding the application range of the MEMS gyroscope.