<p>Spline couplings are widely used in aero-engine rotor systems to connect the turbine and fan rotors. However, due to manufacturing and assembly errors, misalignment of spline couplings is prevalent and adversely affects the secure and reliable functioning of aero-engines. In traditional studies, the spline coupling is often approximated as a nonlinear spring-damper system, disregarding the change in stiffness across its axial length. This paper develops a dynamic model of a rotor system featuring a refined spline coupling, by taking into account the dynamic differences at different positions in the axial direction of the spline coupling. Finally, using the Newmark/Newton–Raphson method with automatic differentiation, the influence of parallel and angular misalignment of the spline coupling on the nonlinear dynamic characteristics of the rotor system is analyzed. This paper demonstrates the necessity of accounting for the dependence of the spline coupling’s dynamic characteristics on axial location, and furthermore establishes criteria for determining both the occurrence and the direction of the spline coupling’s misalignment. These results offer important guidance for the dynamic design and analysis of rotor systems.</p>