Enzymatic saccharification is a key step in the green conversion of lignocellulose to biofuels and other products. A key deficiency in common biocatalytic systems, such as Trichoderma reesei, is the insufficient presence of β-glucosidase (BGL). This study intended to develop an efficient process of BGL production as an enhancement to the T. reesei system. The authors investigated the process optimization of BGL by the mutant strain Aspergillus niger C112, which was previously developed in the authors’ laboratory. The culture medium and process (carbon, nitrogen, temperature, and pH) were optimized for cost-effective BGL production, which led to a maximum BGL activity of 8.91 ± 0.35 U/mL. In addition, the dynamics of the physio-chemical parameters (zeta potential and dissolved organic matter) of the process were studied and showed good correlations to the yield of BGL. Furthermore, a three-dimensional excitation-emission matrix fluorescence spectroscopy was successfully applied for analyzing the component, origin, and dynamics of dissolved organic matter, which contributed to a further understanding and optimization of BGL production.