A novel approach for improving the flame retardancy, smoke suppression and mechanical properties of epoxy resins (EPs) has been proposed by incorporating functionalized hollow mesoporous silica microcapsules (SHP) loaded with phosphorous silane flame retardants (SCA) and coated with polydopamine (PDA) and transition metals. The proposed approach involves a multi-level structure that combines several mechanisms to enhance the flame-retardant properties of EP. The physical barrier provided by silica serves to impede heat and mass transfer during combustion, while the catalytic carbonization effect of phosphorus and transition metals promotes the formation of a protective char layer, which acts as a barrier to further flame propagation. Incorporating a low loading amount of 3 wt% SHP into the epoxy matrix resulted in EP/SHP-3 composites with significantly improved flame retardancy, as evidenced by a limiting oxygen index of 31.5% and a V-1 rating, in contrast to the values obtained for unmodified EP, which were 23.8% and no rating, respectively. In addition, cone calorimeter test (CCT) results indicated that the total heat release, peak heat release rate and total smoke production of EP/SHP-3 decreased by 18.2%, 25.2% and 18.4%, respectively. Moreover, the improved interfacial compatibility facilitated by polydopamine assists in the dispersion and compatibility of the SHP with the epoxy matrix, leading to better mechanical properties. Herein, the addition of 1 wt% SHP to EP significantly improved its mechanical performance, with a 16.7% increase in tensile strength and a 19.2% increase in impact strength. The design of the multi-level structural approach has the potential to provide new ideas for the simultaneous improvement of fire safety as well as mechanical properties of polymers.