This work reports a simple and facile method to prepare novel magnetic mesoporous silica (MMS) materials with high magnetic strength for the convenient and high throughput detection of histidine-tagged enzymes with Ni-doped surfaces. These materials are designed by the incorporation of high-abundance and homogeneously dispersed iron nanoparticles within the mesopores by thermal hydrogen reduction after the incorporation of ferrous ions and demonstrated the selective enrichment and high-throughput recognition of His-tagged enzymes with multi-point anchoring by selective conjugation between the His-tag and Ni ions. Selective His-tagged enzyme enrichment efficiency was compared with nickel-based MMS materials, such as Ni2+-MMS and Ni-MMS, and nickel ion doped silica-coated magnetic nanoparticles (Ni2+-MNPs). The efficiency was calculated to be 100 ± 1.93%, 70.94 ± 1.95%, and 37.03 ± 5.93% for Ni2+-MMS, Ni-MMS, and Ni2+-MNPs, respectively. This method enables a high-throughput and advanced systematic approach for the separation and immobilization of proteins which cover a broad spectrum of polyhistidine-tagged proteins.