In this paper, a novel isolated current-fed DC-DC converter (boost-type) with two input power sources based on multi-transformer structure, which is suitable for fuel cells and super-capacitors hybrid energy system, is proposed and designed. With particular transformer windings connection strategy, the proposed converter can draw power from two different DC sources with lower voltage and deliver it to the higher voltage DC bus or load individually and simultaneously. The detailed operation principle of the proposed converter has been analyzed in dual-input mode and single-input mode, respectively. Furthermore, the method to increase the number of input ports, the magnetic integration structure, and ground loop decoupling are discussed. Experimental results from the lab prototype converter with two DC voltage sources verify the validity of the theoretical analysis and design of the converter.