Naphthalimide-linked covalent organic framework (COF) with two-dimensional (A-COF and B–COF) and three-dimensional structure (M-COF) was designed and applied to self-assembly on PBO fiber surface, and the influences of 2D or 3D COF on interfacial and wave-transparent properties as well as their reinforcing mechanisms of composites were investigated. A-COF and M-COF exhibited higher BET surface area and porosity compared to those of B–COF, and the morphology of 2D and 3D COF respectively presented lamellar nanosheet and random particle aggregation. The dense inner COF layer and numerous nanocrystals were attached on 2D COF@PBO fiber, and 3D COF@PBO fiber surface showed nano-porous structures from M-COF nanoparticle stacking. Compared with pristine PBO fiber composites, transverse fiber bundle tensile (TFBT) strength and interfacial shear strength (IFSS) of A-COF@PBO and B–COF@PBO fiber composites were increased by 38.76% and 51.77%, 37.23% and 43.94% due to lamellar stacking structure of 2D COF, while 15.31% and 19.56% increment for M-COF@PBO fiber composites, which was attributed to the weaker binding force between PBO fiber and 3D COF from interpenetrated structure. The optimal wave transmission efficiency (|T|²) at low frequency was obtained for A-COF@PBO fiber composites, resulting from the highest porosity of A-COF and best interfacial compatibility, while M-COF@PBO fiber composites showed the best |T|² at high frequency due to the higher porosity and scarce electron-coupling phenomenon of M-COF.