Homogeneous Charge Compression Ignition (HCCI) engine is supposed to achieve high thermal efficiency and low emissions. In this study, a new closed loop control system for HCCI engines is suggested to make it practical application. Amount of internal EGR, amount of external EGR and mass of input fuel are used as control factors. And an HCCI engine running on Di-Methyl Ether (DME), which applies the system, is developed. This paper shows the effectiveness of the system confirmed by experimental result and some governing equations. In the result, in-cylinder gas temperature needs to be controlled strictly and the constructed control system is totally available.