The paper presents a graph-matrix model of the biotechnological beer fermentation process based on a systematic approach to describing interactions between substrates, enzymes, products, and environmental regulators. The proposed method combines the structural and kinetic aspects of the process, which makes it possible to formalize the relationship between biochemical reactions, heat and mass transfer, and control actions. The model is implemented in the MATLAB environment and tested in a series of numerical experiments confirming its adequacy to experimental data. It is shown that the graph-matrix representation effectively describes multi-contour interactions and provides a convenient tool for stability analysis, parameter optimization, and the development of automatic fermentation control systems. The obtained results demonstrate the possibilities of integrating graph theory methods, biotechnological modeling and the digital twin of the process, which helps to increase the accuracy of forecasting and controllability of technological parameters at the stages of brewing.