Fuel spray and mixing in linear engines is coupled by dynamics, combustion, and gas exchange, which differs from that in conventional engines. This work presents a system simulation to reveal the multi-process coupling effect of injection position on the fuel spray and mixing of a free piston linear diesel engine (FPLE). A full-cycle fuel spray model which couples with dynamic, combustion, and gas exchange is established to predict the coupled effect on mixture formation. The results indicate that the variable injection position changes the FPLE motion through multi-process coupling effect, resulting in different boundary conditions for fuel spray and mixing. Relatively large injection advance position leads to more residual gas, fast speed, intense turbulence, low gas pressure, and temperature at the moment of injection for mixture formation. The earlier fuel injection generally makes the longer spray penetration, smaller Sauter mean diameter of droplets, less fuel impingement, faster fuel evaporation rate, and more evaporated fuel mass. However, too early injection does not support the above results. Suggesting that in order to achieve homogeneous combustion mode, the large injection advance position injection schedule operation is a good choice for the FPLE due to its long ignition delay duration for fuel atomization, evaporation, and mixing.