In this paper, a new method for the driving of the hydraulic free piston engine (HFPE) is proposed. Hydraulic differential drive achieves the compression stroke automatically rather than special recovery system, which has a great influence on the engine dynamic performance. The purpose of this paper is to solve the key operation and control problems for HFPE to commix fuel with air.HFPE adopts two-stroke loop-scavenging and semi-direct injection. The semi-direct injection nozzle is located in the liner wall inside the main intake port, with the axes oriented towards the piston at the Bottom Dead Center (BDC). Different scavenging pressures and injection angles result in different impacts on the mixture of fuel and air in the cylinder. This study analyzes the changes of the combustion heat release rate by simulation. The result shows that the gasoline back-flow and short circuit loss is minimal, and the mixture of fuel and air is uniform, with the initial pressure of 0.13MPa and injection angle of 120°CA. Moreover, heat release of HFPE is enhanced, which complies with the requirements of the original design. The study can provide the theoretical basis for exploring the scavenging characteristics and operation mechanism of HFPE.