Based on the construction of a three-level index evaluation system of industrial agglomeration and water pollution, models such as coupling coordination were adopted to analyze industrial agglomeration, water pollution, and the development level of coupled coordination between these two aspects and types of relative development in order to strengthen the study of the impact of industrial agglomeration on the water pollution in Henan section of the Yellow River Basin. The results show that the degree of industrial agglomeration of the eight cities in the section is significantly differentiated and generally low, but the average annual growth rate is varied greatly. The comprehensive evaluation index of the water pollution is fluctuating with significant regional differences. The coupling coordination development of industrial agglomeration and water pollution is the coexistence of the antagonistic stage and the running in stage in 2018, 2012, 2015 and 2017, and transformed to the antagonistic stage in 2020. In addition, the relative development types transferred from four types (typeⅠ, Ⅱ, Ⅲ and V) in 2008 to three types (typeⅠ, Ⅱ and Ⅲ) in 2020. The research results can correctly reflect the coupling coordination between the industrial agglomeration and water pollution in Henan section of the Yellow River Basin. For the promotion of high-quality economic development and the achievement of the strategic objectives of “building a resource-saving and environment-friendly society”, it is suggested that the modern industrial structure should be upgraded, the total control of regional water pollution emissions should be implemented, and the enterprises producing heavy pollution should be shut down.