Dissipative structure theory is one of the three new modern theories. In recent years, the theory is demonstrating a promising in social and economic areas. In this paper analyses are conducted on entropy, effect of entropy increasing, and dissipative structure features in logistics system, based on entropy theory and dissipative structure theory. Finally, an entropy differentiation model is set up to analyze the stability of operation and development of logistics system. A simple calculation is also given in this paper. The above finding may provide new study idea for effective management of scientific logistics system.