The multiphase model based on free-energy theory has been experiencing long-term prosperity for its solid foundation and succinct implementation. To identify the main hindrance to developing a free-energy-based discrete unified gas-kinetic scheme (DUGKS), we introduced the classical lattice Boltzmann free-energy model into the DUGKS implemented with different flux reconstruction schemes. It is found that the force imbalance amplified by the reconstruction errors prevents the direct application of the free-energy model to the DUGKS. By coupling the well-balanced free-energy model with the DUGKS, the influences of the amplified force imbalance are entirely removed. Comparative results demonstrated a consistent performance of the well-balanced DUGKS despite the reconstruction schemes utilized. The capability of the DUGKS coupled with the well-balanced free-energy model was quantitatively validated by the coexisting density curves and Laplace’s law. In the quiescent droplet test, the magnitude of spurious currents is reduced to a machine accuracy of 10−15. Aside from the excellent performance of the well-balanced DUGKS in predicting steady-state multiphase flows, the spinodal decomposition test and the droplet coalescence test revealed its stability problems in dealing with transient flows. Further improvements are required on this point.