Entropy is a measure of disorder in a system and is widely used in other scientific and engineering disciplines such as statistical mechanics and information theory. In a chaotic supply chain, the goal is to reduce chaotic behaviors and predict the future of the supply chain. In this case, relationships in a three-tier supply chain are considered in a continuous-time environment. In this paper, the chaotic supply chain is investigated and controlled using the entropy minimization method. Due to the dynamic nature of the supply chain and its chaotic behavior, Poincaré mapping of the system has been prepared by the stroboscopic method. Then, by defining Shannon entropy on the map, the entropy of the system is significantly reduced by the gradient descent algorithm.