The invention discloses a chemical preparing method of molecular recognition of ultratrace explosive TNT molecule based on fluorescence resonance energy transfer, comprising: taking silica ball-shaped nanoparticles as a supporting body; decorating the surface with aminopropyl and 6-FAM hydroxysuccinimide ester; and causing the surface to have special functional group. The invention has the following two steps in the preparing process: firstly, forming a coupled body by covalent coupling of a reacted monomer APTS and fluorescein C1609 at certain reaction condition; then, taking ammonia water as catalyst to hydrolyze and condensate TEOS to obtain silica particles; and finally, mixing the coupling containing excessive APTS with the silica nanoparticles and reacting so as to prepare silica nanoparticles which have expertise identification function to TNT. The silica nanoparticle prepared with the method has large specific surface area and can form a nano-structure probe with high density identification locus, favourable selectivity, favourable sensitiveness and molecular recognition performance.