Large numbers of deep-water drilling practices have shown that more than 60% of deep-water wells have complex leak-off during the drilling process, which poses great difficulties and challenges for the safety and operation time of deep-water drilling. The purpose of this article is to establish a method for predicting the fracture pressure in shallow formations. In this study, the deep-water shallow formation was divided into the upper unconsolidated soil layer, and the lower diagenetic rock layer according to the geotechnical distribution characteristics of the deep-water shallow formation. The location of the transition soil/rock layer zone was determined using the upper soil layer density trend line, and the lower rock layer density log data regression trend line. The deep-water shallow fracture pressure prediction model was established based on the soil/rock transition zone. The shear failure criterion was used above the transition zone, and the tensile failure criterion is used below the transition zone. The shallow fracture pressure of six drilled exploratory wells in the X block from the South China Sea was calculated using this new method and the calculation errors were all less than 3.18%. Moreover, the shallow fracture pressure body in this block was established using the Kriging interpolation method based on six drilled exploratory wells data. This shallow fracture pressure body established here was used to predict nine development wells shallow fracture pressure with a predictive error of less than 1.7% and there were no drilling accidents. The case study demonstrates that the new model can significantly improve the prediction accuracy has good prospects for popularization and application.