For the application of heat exchangers in the aeronautic field, an effective evaluation method is required to support the satisfaction of the multi-aspect design restrictions including the thermal and hydraulic performance, occupied volume, total weight, etc. To weigh the benefit and cost for both heat transfer units and heat exchangers, this study thus proposes three evaluation indexes Rp, RV, and Rm defined by the product of heat transfer coefficient and heat transfer area of unit windward area times pressure drop (hA/(AfrontΔp)), that of unit volume (hA/V) and that of unit weight (hA/m). Considering the factors h and A comprehensively and excluding the influence of mean differential temperature, the three indexes can reflect the low flow resistance, compactness, and lightness characteristics under fixed operating conditions and heat transfer duty requirement accordingly. A validation experiment is carried out and the deviation between the evaluation and experiment results is less than 10.88% for the three indexes. To show the applicability, a detailed evaluation of six different heat transfer units and five types of heat exchangers is conducted. A heat transfer unit selection method based on the new indexes is provided finally for heat exchanger design.