Coal-direct chemical-looping combustion (CDCLC) is a promising coal combustion technique that provides CO2 capture with a low energy penalty. In this study, we developed a three-dimensional Eulerian–Eulerian multiphase full-loop model for simulating the circulation and separation of binary particle mixtures in a novel high-flux CDCLC system. This model comprised a high-flux circulating fluidized bed as the fuel reactor (FR), a counter-flow moving bed as the air reactor (AR), a high-flux carbon stripper, two downcomers, and two J-valves. This model predicted the main features of complex gas–solid flow behaviors in the system. The simulation results showed that quasi-stable solid circulation in the whole system could be achieved, and the FR, AR, and J-valves operated in a dense suspension upflow regime, a near-plug-flow regime, and a bubbling fluidization regime, respectively. The multiphase flow model of binary particle mixtures was used to predict the mechanisms of directional separation of binary particle mixtures of an oxygen carrier (OC) and coal throughout the system. A decrease in the baffle aspect ratio of the inertial separator improved the coal selective separation efficiency but resulted in a slight decline in the OC selective separation; this is believed to be the result of weakening of particle collisions with the baffle. A higher FR gas velocity had a slightly negative effect on the OC selective separation efficiency, but improved the coal selective separation efficiency; this can be attributed to an increase in the particle-carrying capacity of the gas stream. A decrease in the coal particle size led to better entrainment of the coal particles by the gas stream and this increased the coal selective separation efficiency. In real CDCLC applications, the operating variables for separation of binary particle mixtures should be comprehensively assessed to determine their positive and negative effects on the carbon capture efficiency, OC regeneration efficiency, gas leakage restraint, energy consumption, and fuel conversion.