As a promising nanofiller, layered double hydroxides (LDHs) can advance the fire safety of epoxy resin (EP), but so far, due to the problems of dispersion and low efficiency, it has still been a challenge to incorporate the flame retardancy and mechanical properties of EP nanocomposites effectively under the circumstance of a low additive amount. In this work, we take LDHs as the template, via the adsorption of a catechol group and the condensation polymerization between catechol groups and phenylboric acid groups, to prepare a core–shell structured nanoparticle LDH@BP, which contains rich flame-retardant elements. EP/LDH@BP nanocomposites were prepared by introducing LDH@BP into EP. The experimental results indicate that, compared with the original LDH, LDH@BP disperses uniformly in the EP matrix, and the flame retardancy and mechanical properties of EP/LDH@BP are significantly improved. At a relatively low content (5 wt%), EP/LDH@BP reached the rating of V-0 in the UL-94 test, LOI was increased to 29.1%, and peak heat release rate (PHRR) was reduced by 35.9% in cone calorimeter tests, which effectively inhibited the release of heat and toxic smoke during the combustion process of EP. Simultaneously, the mechanical properties of EP/LDH@BP have been improved satisfactorily. The above results derive from the reasonable architectural design of organic–inorganic nano-hybrid flame retardants and provide a novel method for the construction of efficient and balanced EP nanocomposite system with LDHs.