Homogenous charge compression ignition gains attention increasingly because of its high efficiency and low emissions. The combustion phase control has been one of the key technological issues which affect its industrialization of HCCI combustion technology. In recent years, ion current detection technology gains more and more attention due to its simple structure, low cost and its containing of large information of combustion. The signal can be used to detect combustion state and to realize closed-loop control of combustion process according to certain strategies. In this paper, the cycle-by-cycle control strategy of combustion phase was established, employed ion current signals and flexible injection strategy of GDI engine. According to ion current signal phase features in two preceding cycles, fuel amount injected in the next cycle will be adjusted to stabilize combustion. The experiments were done based on a GDI-HCCI test bench. The results show the first injection has obvious effect on both combustion and ion current signal phases. The fuel amount injected in the next cycle can be regulated by first injection. CA50 can be predicted by ion current signal difference dImin. The combustion phase can be controlled within 2 CA. The maximum concentration of HC decreased from 18,000 to 4,000 ppm after combustion phase control was applied. The issue of this study is that fuel amount injected need to be calibrated in different work conditions. The detection circuit needs to be optimized because the signal is a little weak under direct injection method.