The research on modeling and installation performance control of three ducts separate exhaust variable cycle engine has been studied. In this paper, we established the fan, the low pressure and high pressure compressor model based on the stage-stacking method. On this basis, a component-level mathematical model is constructed and the compressor model of adjustable mode selector valve area, the third bypass and its exhaust nozzle mode are established. Besides, the research took the inlet inside and outside characteristic model into consideration. The simulation showed that the engine could be able to modulate the third bypass airflow adaptively by control of fan vane, mode selector valve area, third bypass, and main exhaust nozzle area. It is possible to continuously match the engine’s airflow demand to the inlet’s airflow supply. The results show that compared with the mixed exhaust three ducts variable cycle engine, the inlet spillage drag of the separate exhaust variable cycle engine is reduced by about 18%. Under the condition of supersonic flight, the constant flow control can significantly improve the economy of the engine. Compared with the mixed flow variable cycle engine, the inlet spillage drag of the three ducts separate exhaust variable cycle engine is reduced by about 20%.