This study demonstrated a new procedure for measuring surface tension using molecular dynamics (MD) simulations. The surface tension was measured by the differential capillary rise method for refrigerant mixtures R1123/CF3I and R32/CF3I, which have a low global warming potential. The information of the saturated density in the low-temperature region, which was necessary for data reduction, was supplemented by an MD simulation, which was validated using accurate measurement data near the critical point. The surface tension calculated from the pressure tensor obtained by the MD simulation deviated considerably. However, the surface tension obtained from the simulated density and composition in the vapor and liquid phases by the parachor method was in agreement with the measured values within the measurement uncertainty ranges from 0.15 mNm−1 to 0.35 mNm−1. The simulated density distribution showed positive surface activity at the vapor–liquid interface, indicating that R32 and R1123, with smaller polarities, tended to aggregate on the liquid surface. This helps interpret the empirically postulated decrease in the surface tension of the mixtures due to the concentration of substances with lower surface tension at the vapor–liquid interface.