Abstract: It is the core task of building a beautiful China to meet people’s needs for a beautiful ecological environment, the urban black odorous water bodies are an important source of pollution to the production, living and physical and mental health of urban residents. This study takes the urban black odorous water bodies in the Yangtze River Economic Belt as the research object, comprehensively applies GIS technology and geographic detection methods to identify its spatial structure characteristics and distribution rules, explores influential differences of different factors on the spatial patterns and proposes remediation proposals. As the study shows: (1) The spatial distribution of blacksmelly water bodies in the Yangtze River Economic Belt is in condensed distribution, and the spatial differentiation is obvious. Nuclear density is characterized by independent multiple mononuclear center, secondary centered bands and sporadic distribution; (2) The center of black odorous water bodies are in the central urban areas of Hubei provinces and Hunan provinces. Its system is obviously characterized by scaleless areas, significant fractal features and complexity of spatial structure; (3) Different types of black odorous water bodies are of positive spatial correlation, showing the different patterns of cold and hot spots with “coldness in upstream, and hotness in middle and lower reaches”; (4) The factors affecting the geographical detection of the spatial structure do not contribute significantly to the global scope, and the match of zonal influence factors is obvious. Industrial waste water discharge, domestic water consumption, drainage pipeline length, etc. are significant influencing factors; The elimination and control of the urban black odorous water bodies should be improved by strictly adhering to ecological rules, establishing urban black odorous water bodies management systems and mechanisms, improving the identification and assessment technical standards system, innovating practice renovation, and enriching theoretical research.