The invention discloses a method and a system for improving the performance of a fanjet control system. In an original fanjet control system with an independent first controller K, a second controller Ks is added; therefore, the dynamic characteristics of the system are improved by adopting switching control under the conditions that the characteristics of the fanjet control system are fixed, and PID controller coefficients and sensor and actuator parameters are determined. The method comprises the following steps: firstly, maintaining the original first controller K, and adding the second controller Ks; secondly, selecting the second controller Ks so that the unit step response performance is superior to the performance of the first controller K; thirdly, switching logic designing: under the condition of unit step response, designing a switching logic into a switching condition when output response reaches a certain set threshold value; fourthly, threshold value designing: finding out a threshold value e, so that the accommodation time ts is optimal; fifthly, numerical simulation verification: adopting switching control to improve the dynamic characteristics of the system. The system is small in computing resource occupation, and simple and convenient in designing and debugging.