A microreaction system, which combines chaotic mixing with liquid-segmented flow for the synthesis of hazardous ionic materials, was established. Previous single micro-segmented flow achieved good mixing by increasing the length of the tube via the slow diffusion of the reactants; however, it consumed a long residence time and achieved a low efficiency. Consequently, optimized chaotic micromixing was applied to achieve rapid and excellent initial mixing of the reactants. Thereafter, the optimized chaotic micromixing was combined with the liquid-segmented flow to ensure the homogeneity of particle nucleation/growth while overcoming encrustation challenges. Two tubing coils were employed for the crystal nucleation and growth; they extensively reduced the size of the microreaction system. Additionally, a separation column was designed to achieve on-line recovery of the carrier fluid, followed by on-line separation of the products and waste. Furthermore, the initial performance and design evaluation of the microreaction system were performed. Furthermore, we utilized typical ionic primary explosives, barium-2,4,6-trinitroresorcinate (BaTNR) and lead-2,4,6-trinitroresorcinate styphnate (LTNR), to verify the applicability of the microreaction system. Further, BaTNR and LTNR particles with better crystal morphologies, narrower size distributions, and higher heat release than those of the single micro-segmented flow were prepared to illustrate the advantages of the system. The particle size of BaTNR synthesized by the microreaction system ranged from 5 to 13 μm, while the heat release was 168.7 J·g−1 greater than that of BaTNR prepared by the micro-segmented flow platform. The particle size of LTNR ranged from 30 to 90 μm, while the heat release was 230.1 J·g−1 greater than that of LTNR prepared by the micro-segmented flow platform. Conclusively, this study demonstrated the feasibility of an efficient and safe microreaction system for synthesizing hazardous ionic materials.