The unmatched disturbance is a common disturbance type in practical engineering problems, and traditional control methods are difficult to achieve ideal control performance. Under the background, a control method based on auto-coupling PID(Auto-Coupling Proportional-Integral-Differential, ACPID) control theory is utilized to solve the control problem of a class of nonlinear systems with non-matching disturbances. Firstly, the external disturbances and internal state of this method in the unmatched channel are defined as new unknown states. Meanwhile, the internal dynamics and external disturbances are defined as total disturbances. Then, the system can be transferred to an equivalent unknown linear system. After that, a controlled error system under the reverse phase excitation of the disturbances is constructed. The ACPID control method is employed to design the controller and the closed loop control system model is obtained successfully. The robust stability of the closed-loop control system is also analyzed afterward. In the end, a 2nd order nonlinear system is simulated for verification. It is shown that the ACPD control system not only has good dynamic and steady-state performances, but also has good anti-disturbance robustness with a fast response speed. It can be considered for the application of electric power, transportation, aerospace, and other extensive fields.