For an Automated Manual Transmission (AMT) with clutch inversed for the pure electric vehicle， this paper presented a program that the synchronizer of the AMT was located on the second axis. The seamless gear shifting can be obtained by switching the clutch to the synchronizer. In order to make the output torque of gearbox change smoothly, addressing the vehicle jerk and friction work as the shift performance indexes, different coordinated control strategies were adopted for different stages during shifting: the motor torque remained unchanged in the torque phase, and the clutch torque was controlled coordinately; the speed difference of the clutch was controlled following the target trajectory by motor speed controlled by PID and adaptive fuzzy PID method in the inertial phase. The dynamic model of MATLAB / Simulink was established and simulated, which showed the feasibility and effectiveness of the coordinated control strategy for gear shifting. Compared with the traditional PID controller applied in the inertial phase, the adaptive fuzzy PID controller can effectively improve the shift quality, the max jerk during gear shift and the friction work decreased, the output torque of the transmission changed seamlessly without power interruption, and the comfort of the vehicle was significantly improved.