Under the condition of deep coal seam mining, the multi-layer water-bearing system of the floor and the high-pressure water body worked together, and the fracture expansion and seepage channel evolution showed dynamic changes. The water outburst process was characterized by the coupling change of water pressure, water volume and mining response. Identifying its time-series response law and constructing a targeted control path became the key to preventing and controlling floor water disaster. Based on the monitoring data of working face in Jiulong Mine, this paper analyzed and studied the characteristics of water pressure, water volume and pressure response, and constructed a comprehensive control system of layered target horizon selection, directional branch hole control and grouting control synergy. The results showed that the response of water outburst in deep working face was obviously different in stages, the water pressure changed from stable attenuation to interval fluctuation, the pressure was highly coupled with the water pressure, and the water inflow evolved in three stages with the advance. The engineering application showed that the three-dimensional control system constructed by stratified control, directional branch hole and graded grouting could effectively block the water-conducting fracture and cut off the high-pressure water channel. After control, the water pressure and water inflow decreased greatly and tended to be stable, the permeability of rock mass decreased significantly, and the working face realized safe mining.