Excessive settlement or differential settlement of subgrade will lead to the deterioration of line operational conditions, the reduction of passenger comfort, and even endanger the safety of traffic. Therefore, it is of great significance to study the settlement prediction of subgrade. In order to predict the settlement of foundation under the next level of loading earlier during the embankment construction process, a new method of predicting settlement of soft soil subgrade is proposed. Firstly, based on monitoring results of soft soil foundation, the consolidation parameters of soil layer are back-calculated according to the three-point method. Then, combined with the theory of the consolidation degree of graded loading, the formula that can predict settlement under different loading conditions are derived. Eventually, the practical application of the method is verified by the prediction and comparative analysis of measured settlements based on engineering examples. The result of research shows that the method can predict the foundation settlement after loading during construction of engineering fill. This method has obvious advantages over the traditional curve fitting method and can guide the actual engineering construction.