The Central Committee of the Communist Party of China and the State Council attach great importance to the protection and development of the Yellow River Basin. The "Outline of the Yellow River Basin Ecological Protection and High Quality Development Plan" and the "Yellow River Basin Ecological Environment Protection Plan" clearly propose the requirements of zoning and classification to promote basin environmental protection and governance. Aiming at improving the quality of urban water environment, this paper combines statistical analysis, spatial modeling analysis, geographical Information visualization and other means to carry out research on urban scale spatial management and control countermeasures in the Yellow River basin. Taking 62 cities in the Yellow River basin as the research object, the boundary of control units and urban administrative boundary were fitted by using GIS spatial analysis technology, and the 58 control units in the Yellow River basin designated by the state were further divided into 163 urban control sub units. The article analyzes the water environment quality status of various cities and selects 26 cities with prominent water environment problems within the watershed. An indicator system covering 7 indicators of the crux of water environment problems was established from four aspects, including economic and social development, water resources management, soil and water conservation, and pollution prevention and control. Through spatial modeling analysis, it was found that the rapid economic and social development of cities such as Baotou in Inner Mongolia, Xi 'an in Shaanxi, and Yinchuan in Ningxia led to greater pressure on environmental protection; cities such as Bayannur in Inner Mongolia, Baiyin in Gansu, and Shizuishan in Ningxia were short of water resources and had greater development intensity; cities such as Yulin in Shaanxi, Dingxi in Gansu, and Ordos in Inner Mongolia suffered from serious soil erosion; Lanzhou, Yinchuan, Wuzhong, Luliang, Yulin and other industrial agglomeration cities had greater pressure on industrial pollution prevention and control; Yuncheng, Anyang, Xinxiang and other cities with large populations in the middle and lower reaches had greater pressure on prevention and control of pollution from living sources; Luoyang, Xinxiang in the North China Plain, Weinan, Yuncheng, Linfen in the Fenwei Plain, and Wuzhong, Zhongwei in the Ningxia Hetao Irrigation District had greater pressure on agricultural pollution prevention and control. In view of the above prominent water environment problems, the paper put forward the main control points of urban water environment and suggestions on coordinated control of upstream and downstream, left and right bank related cities.