Corn steep liquor is a waste product from the process of treating corn grain for starch extraction. It is used as a substrate in anaerobic digestion with simultaneous hydrogen and methane production in a cascade of two anaerobic bioreactors. For process research and optimisation, adequate mathematical models are required. So, the authors aim to present a high-quality model of the corn steep liquor process for the sequential production of H2 and CH4. This paper proposes a technique for identifying the best mathematical model of the process using the metaheuristics crow search algorithm (CSA). The CSA was applied for the first time to mathematical modelling of the considered two-stage anaerobic digestion process, using real experimental data. Based on the analysis of the numerical data from the model parameter identification procedures, the influence of the main CSA parameters—the flight length, fl, and the awareness probability, AP—was investigated. Applying classical statistical tests and an innovative approach, InterCriteria Analysis, recommendations about the optimal CSA parameter tuning were proposed. The best CSA algorithm performance was achieved for the AP = 0.05, fl = 3.0, followed by AP = 0.10, fl = 2.5, and AP = 0.15, fl = 3.0. The optimal tuning of the CSA parameters resulted in a 29% improvement in solution accuracy. As a result, a mathematical model of the considered two-stage anaerobic digestion process with a high degree of accuracy was developed.