Cubic FDU-12 type mesoporous silicas with enlarged pores and carboxylic acid (–COOH) functionality in the pore channels (denoted as LP-FTC-x) are synthesized using tetraethyl orthosilicate (TEOS) and carboxyethylsilanetriol sodium salt (CES) as silica sources, Pluronic F127 triblock copolymer as template, and trimethylbenzene (TMB) as pore expander, and utilized them as supports for enzyme immobilization. When the –COOH content is increased from 0 to 30%, the pore size of LP-FTC-x decreases from 23.6 to 11.1 nm, and its particle size decreases from around 2 μm to 600–800 nm. The material exhibits a high papain adsorption capacity (895 mg g−1) with a low leaching rate at pH 8.2 due to the well-defined surface chemistry in the pore channel. The adsorption kinetics and isotherms follow the pseudo-second-order model and the Langmuir isotherm model, respectively. The excellent structural properties of LP-FTC-x are also advantageous for enhancement in stability of enzyme toward the temperature, solution pH, and incubation time variations.