In this paper the ethanol homogeneous charge compression ignition (HCCI) is achieved in a modified single cylinder engine by means of a self-developed fast thermal management system (FTMS), and the ethanol SI/HCCI operation regions are defined. It can be concluded that the thermal efficiency is higher and the NOx emission is lower in the HCCI operation region. In addition, the maximum NOx emission drops by 98%. The ethanol SI/HCCI combustion mode transition is conducted in different conditions near the SI/HCCI operation boundaries. It is likely to realize the transition by the utilization of FTMS. However, it is impossible to complete the transition within one operating cycle under current operation conditions. There are fluctuations in engine speed and brake mean effective pressure during the transition process. In order to reduce the fluctuations during the transition, the initial work concerning the effects of the spark ignition on the transition smoothness is carried out and the investigation indicates that the engine speed and brake mean effective pressure fluctuations cannot be eradicated only through spark ignition. Therefore, the control strategies combined with other factors should be further optimized.