How to optimize the spatial layout of the logistics industry is a challenge faced by every city under the rapid development of e-commerce nowadays. Enterprises and nodes as the core of logistics and their locational formation mechanisms are the key content of the study. Based on the API platform of Gaode Map, the POI data of Zhengzhou City with representative years during 2012–2021 were collected. Using the methods of industry concentration evaluation and nuclear density analysis, the spatial pattern changes of the logistics industry in Zhengzhou in recent years are demonstrated, the differences in location selection of the logistics industry are analyzed, and the analysis of its formation mechanism is made. The results of the study show that: (1) the logistics industry in Zhengzhou has developed rapidly in recent years, forming a “double core” spatial pattern of agglomeration near the four urban areas in the center of the metropolitan area and Xinzheng Airport, with a high degree of coordination in the agglomeration of industries and practitioners; and (2) the layout of logistics nodes is influenced by government planning, and logistics enterprises have strong autonomy in the layout. In the process of industrial agglomeration, the government guides the industry to gradually achieve agglomeration by laying out the transportation environment and providing low-rent land for industrial parks, while logistics enterprises provide services for different types of groups through segmenting specialized markets for different types of groups to provide services.