The invention belongs to the technical field of advanced nanocomposites, and particularly discloses a magnetic mesoporous silica microsphere material with a yolk structure and a preparing method thereof. The macromolecule sol-gel chemical synthesis method is adopted first, magnetic nanoparticles are coated with a polymer resin macromolecule shell, then a mesoporous silica shell is grown on the surface of the polymer resin shell in a non-contact mode by means of the water-oil two-phase method, a surface active agent and an organic solvent are removed through solvent washing and extraction, and finally the magnetic mesoporous silica composite microsphere material provided with ordered mesopore ducts, a large cavity and the yolk structure is obtained. The obtained composite microsphere has the large adjustable cavity, a high specific surface area, the mesoporous shell with a uniform and vertical interface, stable and high magnetic responsiveness, a quite uniform size and high dispersity and has broad application prospects in nanoreactors, catalysis, drug sustained release, large-volume bioseparation and adsorption. The method is simple, raw materials are easy to obtain, and enlarged production is facilitated.