The destruction of shallow aquifers by water-conducting fractures of overlying strata caused by underground coal mining is the most representative form of mining-induced damage in the Yushenfu mining area. It has become an important factor restricting the green mining of coal in the Yushenfu mining area and even the ecological protection and high-quality development of the middle reaches of the Yellow River. As the key scientific problem of water-preserved coal mining, the scientific understanding of the development law and main influencing factors of water-conducting fractures in overlying strata has attracted great attention. Taking the geological occurrence characteristics of the main coal seam in Yushenfu mining area as the prototype, 24 different types of numerical models are constructed with the key characteristics of the overburden structure, such as the number of layers of sandstone in the overburden (sand layer coefficient) and the thickness ratio of sandstone and mudstone in the overburden (sand–mud ratio), as the main variables. By means of numerical simulation experiment and theoretical calculation, combined with field measurement and comparison, the influence of the key characteristics of overburden structure on the development height of water-conducting fracture is studied and revealed. It is proposed that the effective area for the study area to achieve water-preserved coal mining by using the height-limited mining method must conform to the coal seam overburden structure characteristics of “sand–mud ratio 6:4 and sand layer coefficient less than 70%” and “sand–mud ratio 8:2 and sand layer coefficient less than 80%”. The results not only enrich and deepen the research on the influence of geological factors and the law of controlling the development of water-flowing fractures in overlying strata, but also provide theoretical support for the precise protection of groundwater resources in the Yushenfu mining area in the middle reaches of the Yellow River.