The semi-outdoor space (SOS) of a building is a valuable activity space and a microclimate transition zone for occupants. Current parametric and optimization methods for SOS design limit the flexibility and complexity of the design process and lack human-machine interaction, which can lead to design results that do not meet specific requirements and diverge significantly from designer expectations. Therefore, this paper proposes a new dynamic and in-depth human-machine collaborative design method to solve multi-level, complex semi-outdoor space design problems and provide preferable daylighting performance. A phased synergistic method (PSM) is proposed based on hierarchical iterations of design variables. The new method allows for integrating existing design tools and expands their optimization scope to accommodate early design stages with ambiguous requirements. A case study building in Guangzhou, China, is used to showcase the design process and daylighting performance evaluation results. The case study uses the intuitive design method (IDM) and the non-phased method (NPM) results for performance and usability comparison. The study shows that the new method can find spatial combinations with better daylighting performance. It also illustrates the positive effect of adequate human-machine interaction in enhancing building performance and form optimization.