The removal of Zn from wastewater generated from the Zn-based electroplating manufacturing process is essential because the regulation limit of Zn concentration in wastewater is becoming stricter in Japan. However, achieving this through conventional methods is difficult, especially for small and medium enterprises in the plating industry. Therefore, a suitable Zn-removal method with a low cost but high performance and Zn selectivity is required. The application of adsorbents is one possible solution. Mesoporous silica (MS) is a well-known adsorbent with controllable pore size, high specific surface area (SSA), high acid resistance, and ease of surface modification. In this study, we modified the surfaces of MSs with different initial pore sizes by amino groups and investigated their Zn removal performances. The effect of pore size on amine modification using (3-aminopropyl)triethoxysilane and on adsorption performance in a single system was investigated along with Zn adsorption selectivity in the Zn–Ni binary system. Amine-modified MS prepared from MS with an initial pore size of 1.9 nm showed drastically lower performance compared to those prepared from MS with an initial pore size larger than 2.8 nm. Zn-selectivity in the Zn–Ni binary system, containing equal amounts of Zn and Ni, was found to reach a maximum of 21.6 when modifying MS with an initial pore size of 2.8 nm.