Abstract: This paper takes Taigemiao Mining Area in the middle and upper reaches of the Yellow River Basin as the research object, analyzes the relationship between the spatial structure of water-bearing（ｉｓｏｌａｔｅｄ） layer and the development height of water flowing fractured zone, excavates the main control factors affecting the water loss of aquifer in the study area, and introduces the effective thickness index of residual bedrock to construct the water loss risk evaluation system of shallow Cretaceous aquifer. Based on the analytic hierarchy process-entropy weight comprehensive discrimination method, the weight of each main control factor is calculated, and the quantitative evaluation model of the disturbance of deep coal seam mining to shallow aquifer is established. By overlaying the control factor diagrams with different weights, the zoning map of water loss risk in deep coal seam mining is obtained. The zoning results are verified by the measured water inflow of surrounding mines. The results show that the aquifer thickness, water pressure, unit water inflow, and the thickness of residual water-resisting protective layer under the influence of mining are the main controlling factors for the water loss of aquifer in the main coal seam. The northwest and northeast corners of the mining area have good water abundance, and the thickness of residual water-resisting bedrock is thin, resulting in a certain water loss risk in the region. The research results are basically consistent with the actual situation in the field.