In this study, a series of Co3O4 nanoparticle-functionalized mesoporous SiO2 (Co–SiO2) were successfully synthesized via a spontaneous infiltration route. Co species were firstly infiltrated into the confined spaces between the surfactant and silica walls, with the assistance of grinding CoCl3·6H2O and the as-prepared mesoporous SiO2. Then, Co3O4 nanoparticles (NPs) were formed and grown in the limited space of the mesopores, after calcination. Structures, morphologies, and compositions of the materials were characterized by X-ray diffraction, transmission electron microscopy, energy dispersion spectrum, N2 adsorption, and Fourier transform infrared spectra. Results showed that the high content of Co (rCo:Si = 0.17) can be efficiently dispersed into the mesoporous SiO2 as forms of Co3O4 NPs, and the structural ordering of the mesoporous SiO2 was well-preserved at the same time. The Co3O4 NP functionalized mesoporous SiO2 materials were used as Fenton-like catalysts for removing methylene blue (MB) from aqueous solutions. The catalyst prepared at rCo:Si = 0.17 could completely remove the high-concentration of MB (120 mg·L−1), and also showed an excellent performance with a removal capacity of 138 mg·g−1 to 180 mg·L−1 of MB. Catalytic mechanisms were further revealed, based on the degradation results.