A two-stage Stirling cooler driven by two independent displacers is numerically investigated so that the effect of the independent displacers on the performance of the Stirling cooler has been thoroughly examined. A conventional Stirling cooler with a step displacer is compared to the performance of the two-stage Stirling cooler with the independent displacers. Both of them possess the same cooling capacities of 30 W at 100 K and 10 W at 50 K simultaneously with the same diameters of the displacers. The designed two-stage Stirling cooler requires the input PV power of 346 W with the step displacer and that of 325 W with the independent displacers. It is confirmed that the thermodynamic efficiency of two-stage Stirling cooler can be improved with the independent displacers. The strokes of the step displacer and the second displacer of the independent displacer configuration are changed by adjusting the spring stiffness of the displacer. While the cooling capacities of the first and the second stages can be varied in the same way by the spring stiffness, the independent displacer configuration allows each stage’s cooling capacity to vary more flexibly. The relevant thermodynamic effect of the independent motions of the displacers is studied and discussed in detail to present the potential benefit of achieving high efficiency in a large-scale Stirling cooler.