Magnetic nanospheres are becoming a promising platform for a wide range of applications in pharmacy, life science, and immunodiagnostics due to their high surface area, ease of synthesis and manipulation, fast separation, good biocompatibility, and recyclable performance. In this work, an innovative and efficient method is developed by in situ reducing and growing Ni(OH)2 for the preparation of dendritic mesoporous nanocomposites of silica@Fe3O4/tannic acid@nickel hydroxide (dSiO2@Fe3O4/TA@Ni(OH)2). The flower-like nanospheres have good magnetic response, large surface area, and high histidine-rich protein (His-protein) purification performance. The dSiO2@Fe3O4/TA@Ni(OH)2 nanospheres were synthesized on the basis of a φ(NaSal/CTAB) of 1/1 and a mass of ferrous chloride tetrahydrate of 0.3 g, resulting in a saturation magnetization value of 48.21 emu/g, which means it can be collected within ∼1 min using a magnetic stand. Also, the BET test showed that the surface area is 92.47 m2/g and the pore size is ∼3.9 nm for dSiO2@Fe3O4/TA@Ni(OH)2 nanocomposites. Notably, the nickel hydroxide with unique flower-like structural features enables the combination of a large number of Ni2+ ions and His-proteins for high performance. The isolation and purification experiments of the synthesized dSiO2@Fe3O4/TA@Ni(OH)2 were performed by separating His-proteins from a matrix composed of bovine hemoglobin (BHb), bovine serum albumin (BSA), and lysozyme (LYZ). The result showed that the nanospheres have a high combination capacity of ∼1880 mg/g in a rapid equilibrium time of 20 min, which was selective for the adsorption of BHb. In addition, the stability and recyclability of BHb are 80% after seven cycles. Furthermore, the nanospheres were also used to isolate His-proteins from fetal bovine serum, proving its utility. Therefore, the strategy of separating and purifying His-proteins using dSiO2@Fe3O4/TA@Ni(OH)2 nanospheres is promising for practical applications.