Homogeneous charge compression ignition has proven to be both highly efficient and to operate with ultra-low NOx raw emissions. However, homogeneous charge compression ignition combustion is a dynamic process due to strong cycle-to-cycle coupling effects caused mainly by the residual gas. Compared to conventional spark-ignited and diesel engines, the lack of direct mixture composition and ignition control increases the challenge of combustion instabilities, especially at boundary conditions. To stabilize the combustion process, real-time in-cylinder combustion diagnostics and control are often used. In this study, for the first time, ion current detection technology and direct water injection are combined for homogeneous charge compression ignition combustion control. By analyzing the return map of the crank angle at 50% cumulative heat release under unstable conditions, it was identified that a misfire or incomplete combustion is usually followed by knocking-like early combustion with high cylinder pressure gradients. Through the correlation analysis between ion current and combustion, a cycle-to-cycle closed-loop control strategy was developed and implemented on a rapid control prototyping engine control unit. Real-time calculated ion current parameters were used to predict the 50% cumulative heat release position of the next cycle and prevent early combustion by direct water injection. The calculation results and controller performance were validated on a single-cylinder research engine. With the controller activated, the standard deviation of 50% cumulative heat release and dynamic programming to the max could be reduced by 19% and 11%, respectively. The coefficient of variation of indicated mean effective pressure was reduced by 12%. A slight increase in indicated mean effective pressure after activating the controller also shows the potential for efficiency improvement. Moreover, not only early combustion is controlled, but also late combustion is significantly reduced.