A large numbers of deep-water drilling practices have shown that more than 60% of deep-water wells have the 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 the soil/rock transition zone. Shear failure criterion was used above the transition zone and tensile failure criterion is used below the transition zone. The shallow fracture pressure of 6 drilled exploratory wells in the X block from the South China Sea were 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 6 drilled exploratory wells data. This shallow fracture pressure body established here were used to predict 9 development wells shallow fracture pressure with a predictive error 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.