The rational zoning of aquatic ecological function fully reflects the water environment management idea of “grading, classification, zoning, and staging,” which is an important basis for the management of aquatic environment and water ecosystem. In this paper, the characteristics of natural environment, water ecological factors, and socio-economic activities of the Songhua River basin are analyzed by data fusion technology on ArcGIS software. Based on the three levels of aquatic ecological function in Songhua River Basin, the ecological function importance level of five kinds of aquatic ecological function was evaluated, including habitat maintenance, water conservation, biodiversity maintenance, agricultural production maintenance, and urban support. According to the evaluation results, the Songhua River Basin was divided into 65 water ecological functions of level 4 zoning. Compared with previous methods, this study utilized the data fusion technology, which considered the natural ecology and the impact of social economic factors on the function importance level. The process of the evaluation is more intuitive, and the results are more reasonable and effective. Based on the analysis of the zoning results, this paper provides some reasonable suggestions for the management of the aquatic environment of Songhua River Basin. The results can help identify the characteristics and functional status of the water ecosystem, lay a foundation for the river health evaluation, and provide an important basis for the scientific management of the aquatic ecosystem in the Songhua River Basin.