The invention discloses a core-shell-structured fluorescent mesoporous inorganic oxide nanoparticle and a preparation method thereof. The fluorescent mesoporous inorganic oxide nanoparticle is of a core-shell structure, wherein the core is a small compact solid ball and a silicon oxide, iron oxide or manganese oxide inorganic nanoparticle, and the shell is an organic fluorescent group-modified mesoporous structure. The organic fluorescent group of the shell is an organic fluorescent double-end silicon source structure which is as shown in (R'O)3Si-R-Si(R'O)3, wherein R' is a C1-4 alkyl group, and R is fluorophore. The preparation method for the core-shell-structured fluorescent mesoporous inorganic oxide nanoparticle comprises the following three steps: 1) preparation of the inorganic oxide inorganic nanoparticle; 2) preparation of core-shell-structured oxide nanoparticle; and 3) removal of a mesoporous channel template in the shell. The invention has the following beneficial effects: the nanoparticle has structured morphology and good monodispersion; a skeleton is modified by organic fluorophore and has controllable fluorescence properties; and reaction conditions are mild, and preparation is simple and can be easily repeated.