The Non-Synchronizer Automated Mechanical Transmission (NSAMT) demonstrates a straightforward structure and cost-effectiveness; however, the primary obstacle to its widespread application lies in NSAMT shift control. The implementation of active angle alignment effectively addresses the issue of shifting quality, but achieving active angle alignment necessitates precise tracking of the planned shifting curve by the gear-shifting actuator. To tackle the control problem of accurate tracking for NSAMT shift actuators, this paper initially analyzes the structure and shift characteristics of the NSAMT. Based on this analysis, a physical model is established using Amesim, incorporating a drive motor, two-gear NSAMT, shift actuator, sleeve, and DC motor model. An extended state observer (ESO) is designed to mitigate unknown interference within the system. Furthermore, an active angle alignment control algorithm based on “zero speed difference” and “zero angle difference” for double target tracking is constructed while planning the axial motion trajectory of the sleeve. The Backstepping algorithm is employed to successfully track and regulate this planned trajectory. Finally, through Hardware-in-the-Loop testing, we validate our proposed control strategy, which demonstrates consistent results with simulation outcomes, thereby affirming its effectiveness.