The invention provides a three-dimensional collaborative design method for spacecraft final assembly and thermal design. The digital collaborative design comprises a configuration level, a cabin section level, a layout level and a final assembly level. Collaborative design by a mechanical overall design department and a thermal control design department is mainly conducted on the cabin section level, the layout level and the final assembly level. According to the three-dimensional collaborative design method, a three-dimensional digital model system is adopted, and constitution of the spacecraft model system and specific content of models at all the levels are clarified; according to the constitution of the model system, it is clarified that the thermal control design department and the mechanical overall design department conduct collaborative design according to appointed division of work, so that the design efficiency is improved; step-by-step transmission of overall design parameters and top-level design information is achieved, it is guaranteed that detailed design models meet the requirements of overall design indicators and parameters, and the accuracy of a final model is guaranteed.