The turbulence and overshot come from switching tracking mode in theodolite system are investigated.A math model of the system switching is established and the reasons for these problems are figured out in theory.In order to improve the characteristics of transient response,an initial value compensation method based on compensating the difference outputs between current controller and former controller is proposed and compensated math model and response for this system are given.Simulation results indicate that the turbulence of miss-distance is restrained within 0.003°,which improves the dynamic process of the system and suppresses the turbulence in switching track mode.