Organic flame retardant 9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide (DOPO) was used to decorate the pores of mesoporous silica (m‐SiO2) nanospheres to prepare a new composite flame retardant (DK‐SiO2). The content of DOPO in DK‐SiO2 is about 17 wt%. Due to the chemical bonding, DK‐SiO2 not only enhances the flame retardant performance, but also effectively avoids adverse effects of DOPO on the glass transition temperature and mechanical properties of epoxy resin (EP). At 9 wt% loading, the limiting oxygen index of the EP increased from 25.7 to 31.2, and successfully passed the UL‐94 V‐0 rating. Besides, DK‐SiO2 can significantly reduce the peak heat release rate, total heat release, and total smoke production of EP, with reductions of 26%, 32%, and 20.8%, respectively. Compared with the simple blended sample, DK‐SiO2 not only has better flame retardant performance but also shows significant advantages in thermodynamic properties. The glass transition temperature, impact, and tensile strength, as well as storage and flexural modulus have been improved. This excellent flame retardant performance is mainly attributed to the gas‐condensed synergistic flame retardant mechanism between DOPO and m‐SiO2. The good thermodynamic performance is due to the excellent dispersion of DK‐SiO2 nanospheres in the EP.