The prediction and optimization of transportation cost of hazardous chemicals is the key to improve the profit and competitiveness of chemical enterprises. Based on the cost optimization theory, this paper establishes the logistics cost control and optimization system of chemical enterprises, calculates and optimizes the logistics cost of chemical enterprises by using the method of quota analysis, and takes a chemical enterprise in Jiangsu Province as an example. The results show that the productive idle capacity of the delivery center is the highest in this chemical enterprise. The difference between the rated cost and the actual cost of the warehouse center is RMB 0.813, and the difference between the rated cost and the cost of the delivery center is RMB1.54. The logistics cost optimization of hazardous chemicals in warehouse center and delivery center is the key to control the logistics cost of the chemical enterprise. The study of logistics cost control has important guiding significance for chemical enterprises to tap logistics cost profit.