To ensure the successful implementation of the separation, evacuation, and return processes of manned spacecraft after long-term docking at the space station, regular on-orbit health assessments must be conducted. Based on this requirement, a technical method for evaluation through autonomous on-orbit testing is proposed. First, the docking status and characteristics of the manned spacecraft’s systems, such as information management, crew environmental control, thermal control, power management, docking function, attitude, and orbit control function, are described. Then, the functional requirements for the separation, evacuation, and return of the manned spacecraft, such as the relative measurement, the relay communication, TT&C and data transmission, image and voice, instrument display and alarm, and the attitude measurement, are analyzed. Subsequently, the on-orbit testing system, test items, test procedures, and test methods for health assessment are detailed. It also provides the design of TT&C support, the design of energy support, and the main principle explanation for autonomous on-orbit testing of the system.