The logistics transportation optimization scheduling method based on intelligent decision system is the development trend of the future logistics industry. Based on the intelligent decision-making technology of dangerous goods logistics, and also the combination of wireless radio frequency identification (RFID) and wireless sensor network (WSN), this paper constructs a decision-making method for hazardous chemicals transportation based on intelligent logistics system, and for the defects existing in the current transportation process of hazardous chemicals. Then. it proposes the intelligent optimization scheduling model of hazardous chemicals logistics path, which optimizes the information collection methods in traditional hazardous chemicals logistics, realizes the dynamic monitoring of dangerous goods logistics, and effectively reduces the occurrence probability of hazards. Meanwhile, in this paper, the traditional Petri net has been improved to construct a Petri net-based logistics process optimization algorithm with workflow weighting performance. This algorithm can describe and model the whole process of logistics in a hierarchical way, perform multi-dimensional performance analysis on the logistics process, and accurately find the defects in the logistics process, so as to get the optimal dangerous goods logistics distribution strategy. The example verification results show that the proposed model in this study has high practicability, which can provide the optimal transportation decision-making scheme for hazardous chemicals under the complicated conditions of multi-operation nodes, multi-flow direction and multi-transport modes.