Controlling the phase-separated structure of polymer alloys is a promising method for tailoring the properties of polymers. However, controlling the morphology of phase-separated structures is challenging. Recently, phase-separated structures have been fabricated via 3D printing; however, only a few methods that enable on-demand control of phase separation have been reported. In this study, laser-scanning stereolithography, a vat photopolymerization method, is used to form a phase-separated structure via polymerization-induced microphase separation by varying the scanning speed and using macro-reversible addition/fragmentation chain transfer (macro-RAFT) agents with different average molar masses, along with multiarmed macro-RAFT agents; such structures were used to fabricate 3D-printed parts. Various phase-separated morphologies including sea-island and reverse sea-island were achieved by controlling the laser scanning speed and RAFT type. Heterogeneous structures with different material properties were also achieved by simply changing the laser scanning speed. As the deformation due to shrinkage in the process of cleaning 3D-printed parts depends on the laser scanning speed, shape correction was introduced to suppress the effect of shrinkage and obtain the desired shape.