A composite intake system and method of operating a rotary engine with variable intake manifold is provided. The system includes two switching valves in a secondary intake switching tube to change the intake method. When the rotary engine works under low speed conditions, it adopts the long intake manifold and the side-intake mode. When the rotary engine works under medium and high speed conditions, it uses the short intake manifold and the composite-intake mode. When the rotary engine works under ultra high speed conditions, it takes the short intake manifold and the peripheral-intake mode.