Abstract: This study aims to address roof support crushing and water gushing caused by the stoppage of thin coal seam working face in low-lying section. With 1599 working face of Xuyong No.1 Coal Mine as the subject of research, this study conducted theoretical analysis, physical similarity simulation, numerical simulation and field measurement to investigate the development patterns of overburden rock cracks before and after stopping mining and analyze the fracture instability type and mechanical mechanism of key strata after its extension to the aquifer. Results indicate that the roof above the low-lying segments of the coal seam is basically in a water-rich state at a depth of 0~40 meters. Before the working face enters the low-lying section in mining, the sub-key strata 1 and 2 break sequentially and form a stable beam structure, with the overburden fractures mainly consisting of separation fractures. After the working face enters the low-lying section and stops mining, the separation fractures in the overburden strata continue to develop laterally, while the vertical fractures develop to communicate with the Changxing limestone aquifer, forming a complete water inrush channel. The water-affected sub-key strata 1 and 2 exhibit shorter periodic fracture distance and higher development height of the caving zone and fracture zone. Therefore, after the working face enters the low-lying section for mining, the fracture of sub-key stratum 2 and subsequent sliding instability are triggered by insufficient support force of the supports, slow advancing speed, and water deterioration of sub-key stratum 2. This leads to roof caving and water inrush in the 1599 working face. In this light, this study proposes a combined control scheme of medium-deep hole grouting and advanced drainage for the roof strata of the low-lying section in the 1599 working face.