Mesoscale phenomena are ubiquitous in multiphase reaction systems where the material, reactor and system levels all feature the mesoscale structures, such as molecular assemblies, particle (bubble/droplet) clusters, or reactor networks, respectively. Mesoscale problems are essential to a more fundamental understanding of momentum, mass and heat transfer in the classical study of transport phenomena, and to the mixing, residence time distribution and rate-limiting analysis in the chemical reaction engineering, yet they are beyond the scope of those classical textbooks of chemical engineering. In this presentation, I will highlight a heuristic mesoscale modeling approach for multiphase reactor systems, starting from a conceptual Energy-Minimization Multiscale (EMMS) model and ending at the stability-constrained multifluid CFD model. While the stability condition determines the direction of system evolution, the stability-constrained CFD further describes the dynamics of structure evolution. Then this theory is applied to the simulation of gas-solid fluidization and gas-liquid bubble column reactors, with further extension to gas-liquid-solid three phase flow and stirred tanks. Several industrial applications on meso-scale modeling in liquid-solid polyethylene reactors and liquid-liquid emulsification systems will also be highlighted.