Graph theory is a well-established mathematical concept that is widely used in numerous applications such as in biology, chemistry and network analysis. The advancement in the theory of graph has led to the development of a concept called autocatalytic set. In this paper, a mathematical modeling technique namely graph-based dynamic modeling of palm oil refining process is introduced. The system parameters are identified in detail in the beginning of the paper. The parameters involved are the chemical compounds used or produced during the refining process. These identified parameters are then modeled as the vertices and edges of the graph. The dynamicity of the system is then simulated and analyzed. The system is simulated using MATLAB software programing. The two final products produced by the refining process agreed with results obtained from other published methods. Hence, the effectiveness and simplicity of the model are established.