A three-dimensional (3-D) frequency selective surface (FSS) based on multiple square coaxial waveguides (SCWs) is proposed, which realizes a dual-bandpass response with close band spacing. In the unit cell of the proposed 3-D FSS, two concentric SCW propagation paths and one parallel-plate waveguide (PPW) propagation path are constructed by utilizing three square metallic tubes. Each SCW propagation path intrinsically generates one transmission pole by the square slot resonance, and the PPW propagation path produces another transmission pole by the halfwavelength resonance. In addition, two transmission zeros are introduced due to the counteraction of out-of-phase signals between different paths, improving the frequency selectivity. After properly adjusting the design parameters, two desired passbands are obtained around 4.4 and 4.845 GHz, and the band ratio is only 1.1. Through the electric-field distributions, equivalent circuit model and parameters study, the operating principle of the proposed 3-D FSS is investigated. A prototype of the proposed 3-D FSS is fabricated and measured. The measured results show that the proposed design can achieve a stable response under the incident angles up to 45°for both TE and TM polarizations.