For a compression ignition (CI) free piston engine linear generator (FPLG), injection timing is one of the most important parameters that affect its performance, especially for the one-stroke starting operation mode. In this paper, two injection control strategies are proposed using piston position and velocity signals. It was found experimentally that the injection timing’s influence on the compression ratio, the peak in-cylinder gas pressure and the indicated work (IW) is different from that of traditional reciprocating CI engines. The maximum IW of the ignition starting cylinder, say left cylinder (LC) and the right cylinder (RC) are 132.7 J and 138.1 J, respectively. The thermal-dynamic model for simulating the working processes of the FPLG are built and verified by experimental results. The numerical simulation results show that the running instability and imbalance between LC and RC are the obvious characters when adopting the injection strategy of the velocity feedback. These could be solved by setting different triggering velocity thresholds for the two cylinders. The IW output from the FPLG under this strategy is higher than that of adopting the position feedback strategy, and the maximum IW of the RC could reach 162.3 J. Under this strategy, the prototype is able to achieve better starting conditions and could operate continuously for dozens of cycles.