Separate type heat pipe heat exchangers are often used for large-scale heat exchanging. The arrangement of such a heat exchanger conveniently allows heat input to and output from the heat exchanger at remote locations. The traditional method of designing an ordinary HPHE (heat pipe heat exchanger) is commonly applied in the separate type exchanger design, but the calculations have to be carried out separately, which makes it very complicated. In this work, the ε-NTU (effectiveness-Number of Transfer Units) method was applied for optimization analysis of single- or multi-level separate type heat pipe heat exchangers. An optimizing formula for single-level separate type heat pipe heat exchangers was obtained. The optimizing principles of effectiveness-NTU and heat transfer rate by the equal distribution method for multi-level separate type heat pipe heat exchanger are presented. The design of separate type heat pipe heat exchangers by the optimizing method is more convenient and faster than by the traditional method.