Cubic mesoporous silica nanoparticles (MSNs) with the SBA-1 moiety, functionalized with carboxylic acid (–COOH) groups as well as enlarged mesopores, are successfully synthesized using tetraethyl orthosilicate (TEOS) and carboxyethylsilanetriol sodium salt (CES) as silica sources, complexes formed by polyacrylic acid (PAA) and hexadecylpyridinium chloride (CPC) as templates, and trimethylbenzene (TMB) as pore expander. The successful incorporation of organic functionalities are confirmed by 13C and 29Si solid-state NMR. The structural properties of cubic mesostructures are characterized by powder XRD, N2 adsorption-desorption isotherms, and TEM measurements. The prepared MSNs exhibit a remarkably high adsorption capacity of 1138 mg g−1 at pH 8.2 when they are used as the supports to immobilize papain. Both factors of the large pore size of the support and the favorable electrostatic attractions between the carboxylate groups on the adsorbent surface and the papain molecules play important roles in reaching such a high adsorption capacity. The immobilized papain possesses better thermal stability, pH tolerance, and heat resistance in comparison to the free papain. The materials are also used for selective adsorption of a single protein (papain) from the binary mixture of two different types of proteins (papain and hemoglobin). Our results demonstrate that proteins such as papain and hemoglobin with different isoelectric points and shapes can be effectively separated from their binary mixture by simply tuning the pH of the buffer.