Polymorphic transformation is of paramount importance as it significantly influences the physical, chemical, and functional properties of materials, with profound implications in fields ranging from advanced materials engineering to high-energy material science. However, there is difficulty in understanding transformation mechanisms, achieving precise control over transformation processes, and addressing the stability of polymorphs. This work sets its sights on 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20), a typical polycrystalline explosive, and innovatively embarks on the development of a control strategy for polymorphic transformation from both mechanistic and experimental perspectives by microfluidics. We delve into the microscopic transformation mechanisms from the alpha-form to the beta-form and eventually to the epsilon-form, utilizing molecular dynamics simulations incorporating thermodynamic and kinetic principles. To control these transitions, a custom-engineered coaxial micromixer was developed, leading to the establishment of an advanced microfluidic system for polymorph control. The groundbreaking mechanism was validated by scrutinizing the influence of microfluidic conditions on the polymorphic transformation, facilitating a continuous and efficient transition from alpha-CL-20 to epsilon-CL-20-PBX. Notably, thermal decomposition tests provided further endorsement, confirming the superior storage safety and reliability of epsilon-CL-20-PBX. The findings offer an unprecedented understanding of the polymorphic transformation of explosive materials and open new avenues in the manipulation of polycrystalline materials.