The force of a marine diesel and its shafting are complex. With effects between structure assembly and hull deformation, shaft misalignment often occurs, which can lead to serious accidents such as bearing wear, coupling fracture, and crankshaft fracture. Due to the influence of structural and operational conditions, traditional vibration time-frequency analysis methods struggle to accurately detect and quantify shafting misalignment. Additionally, the characteristic of power and double frequency is easy to be aliased with other fault features and causes misjudgment. Therefore, a model for misalignment morphological characteristics is developed based on the structural features of misaligned shafting. An online detection scheme is proposed to account for misalignment patterns and mechanical structure effects. The research focuses on the diesel output shaft, and a six-degree-of-freedom fault simulation test bench is established for experimental verification of the misalignment detection method. Furthermore, a self-healing control scheme for shafting misalignment faults is proposed and validated through experiments, enabling online self-healing control of such faults. The data demonstrates that the misalignment detection method based on shafting morphological characteristics can achieve online detection of misalignment under different working conditions, with an accuracy rate exceeding 90%. The self-healing control device driven by servo electric cylinder can reduce the misalignment of shafting by more than 75% within 10 s.