To realize the functions of infrared transparent as well as radar double– pass Band, A Y loop and Y slot compound element Frequency Selective Surface (FSS) structure is proposed, which takes an infrared transparent inductive mesh as a substrate. The proposed structure is analyzed based on Galerkin spectral method. The transitivity of infrared (3um-5um) as well as the radar double passed band with two resonance frequencies (31GHz and 54GHz) is discussed. The result reveals that this structure has function of infrared transparent as well as stable radar double–band filter with effective shielding effect on S-band and C-band radar electromagnetic waves. The design with multiple passband is suitable for radar/IR composite guidance and it also offers a kind of new thinking way of design for multi-mode compound guidance systems.