In this study, experimental and numerical investigations of a homogeneous charge compression ignition (HCCI) combustion engine were performed using alcohol-gasoline fuel blends and two-stage direct injection (TSDI) strategy. A diesel engine was modified to operate as an electronically controlled HCCI-DI engine. TSDI strategy was applied by fixing the first injection timing in intake stroke and varying the second injection timing close to the compression top dead center (TDC). The selected fuels were pure gasoline and four different blends of ethanol and methanol with gasoline, namely E10, E20, M10 and M20. The effects of the second injection timing and alcohol-gasoline fuel blends on the HCCI combustion and emissions were investigated at constant engine speed and high equivalence ratio for the same energy input. CFD simulations were performed using AVL Fire code and CFD results were compared with the experimental results of the HCCI-DI engine. Cylinder gas pressure, rate of heat release (ROHR), maximum cylinder gas temperature, CO and NOx emissions were investigated numerically. Visual information about the in-cylinder temperature distribution and NOx emissions were provided from images taken from the CFD model. It can be understood from both experimental and CFD studies that combustion phase can be most effectively controlled by changing the second fuel injection timing for all fuel blends. Adding alcohol to gasoline helped to decrease NOx emissions while keeping the maximum cylinder gas pressure stable compared to pure gasoline.