In this study, the effects of the number of injection holes on the in-cylinder mixing characteristics and combustion performance of a low-load methanol direct-injection free-piston engine generator (FPEG) were systematically investigated through a combination of numerical simulation and experiment. The results show that the increase in the number of injection holes significantly optimizes the in-cylinder equivalence ratio distribution, and the percentage of the extreme equivalence ratio region is reduced dramatically; at the same time, the increase in the number of holes shortens the spraying, the rise in the number of nozzles shortens the spraying time, prolongs the premixing time of oil and gas, and improves the mixing uniformity. In terms of combustion performance, the three-hole nozzle exhibits the best overall performance, with a 19% increase in peak cylinder pressure compared to the dual-hole nozzle, an indicated thermal efficiency above 40%, and the shortest combustion duration. In contrast, the six-hole nozzle produces an excessively dispersed spray, resulting in a dilute mixture in the vicinity of the spark plug, prolonged ignition delay, and lag in the cylinder pressure phase.