In the present study, to find the optimal performance of a combined RE-1000 Free Piston Stirling Engine (FPSE) with a three-phase Permanent Magnet Linear Synchronous Machine (PMLSM), two different control methods were developed. To convert the produced mechanical power of the FPSE to the electrical one, generally, it should be coupled with a linear generator. Here, a three-phase PMLSM was chosen to convert the linear movement of the FPSE to electricity. The control of the FPSE system was also done through this generator using velocity control. It is possible to obtain the optimal system behavior based on the identification of the adapted velocity reference value. Based on two different methods, the FPSE-PMLSM optimum working point was determined. In the first method, an open-loop sinusoidal wave was assumed as the reference velocity, and its amplitude and frequency were optimized. In the second method, the reference velocity was identified using closed-loop feedback of the electromagnetic force, and the optimal feedback coefficient was found. The results show that apart from the advantages and disadvantages related to each method, the optimized point was almost identical.