Rational design and synthesis of noble metal nanomaterials with desired crystal phases (atomic level) and controllable structures/morphologies (mesoscopic level) are paramount for modulating their physiochemical properties. However, it is challenging to simultaneously explore atomic crystal-phase structures and ordered mesoscopic morphologies. Here, we report a simple synergistic templating strategy for the preparation of palladium-boron (Pd-B) nanoparticles with precisely controllable crystal-phases and highly ordered mesostructures. The engineering of crystal-phase structures at atomic levels is achieved by interstitially inserting metallic B atoms into face-centered cubic mesoporous Pd (fcc-mesoPd) confined in a mesoporous silica template. With the gradual insertion of B atoms, fcc-mesoPd is transformed into fcc-mesoPd(5)B, hcp-mesoPd(2)B with randomly distributed B atoms (hcp-mesoPd(2)B-r), and hcp-mesoPd(2)B with an atomically ordered B sequence (hcp-mesoPd(2)B-o) while preserving well-defined mesostructures. This synergistic templating strategy can be extended to engineer crystal-phase structures with various mesostructures/morphologies, including nanoparticles, nanobundles, and nanorods. Moreover, we investigate the crystal-phase-dependent catalytic performance toward the reduction reaction of p-nitrophenol and find that hcp-mesoPd(2)B-o displays much better catalytic activity. This work thus paves a new way for the synthesis of hcp-Pd2B nanomaterials with mesoscopically ordered structure/morphology and offers new insights of fcc-to-hcp evolution mechanisms which could be applied on other noble metal-based nanomaterials for various targeted applications.