Wallago Attu and Pangasius Sanitwongsei are two types of fish with huge potential for agricultural economic development and commercial value in the freshwater ecosystems of the Mekong Delta region. However, environmental changes and overfishing have threatened these species’ population dynamics. Our main concern is to improve the understanding of human impact on the ecosystem’s stability. A new model is constructed to represent the food chain involving the two fish species and their common prey. Some notable parameters, such as the harvesting rate of humans and the intraguild predation rate, will be analyzed more closely. Numerical analyses were performed to analyze the existence and stability of five equilibrium points and investigate the impact of varying model parameters. Simulation results and bifurcation diagrams provided insights into how changes in ecological factors influence the long-term population trends of the species. Several complex system behaviors have been observed as the environment changes, causing increased predatory ability of Pangasius Sanitwongsei species. The coexistence of the predators and the prey populations is possible if the harvesting rate falls within the range of 14% to 43%, which requires strict management of fishing activities.