Core-shell structured explosives possess improved material properties and the multifunctionality to combine various components, which can provide a way to achieve a balance between energy and safety in the modification research of energetic materials. To achieve this goal, a microdroplet self-assembly strategy has been proposed, which is a preparation platform that combines microdroplet technology with in-situ encapsulation technology. Octogen (HMX) and binder (F2604) were chosen as the core, and polydopamine (PDA) as the shell, to prepare high-quality HMX/F2604@PDA core-shell microspheres with different shell thicknesses by controlling the PDA polymerization time. The effect of PDA polymerization time on the coating effect, morphological structure, and performance of the core-shell microspheres was studied in depth. The results show that PDA can effectively improve the surface defects of HMX/F2604 microspheres, thereby exhibiting high sphericity, excellent flow performance, and higher bulk density. Moreover, the PDA shell can form a comprehensive physical barrier on the surface of the HMX polymer binder microspheres, delaying the polymorphic transformation of HMX crystals, and postponing the thermal decomposition temperature, showing higher activation energy, and greatly enhancing thermal stability. When the PDA thickness is 4.96 mu m, the mechanical sensitivity of the core-shell microspheres H@P-15 is reduced by 22 %, and safety is improved. Additionally, combustion tests indicate that core-shell microspheres with a PDA thickness of 3.11 mu m undergo rapid combustion with intense reactions. This study, distinct from previous reports, achieves controllable regulation of the PDA shell and provides a way and reference value for the preparation and structural design of spherical core-shell structured explosives.