Geometrical nonlinearity of the soft soil and the deviation of water flow in the soft clay from Darcy’s law have been well recognized in practice. However, the theory of consolidation, which can account for both the geometrical nonlinearity and the non-Darcian flow, has not been reported so far. In this contribution, a model for the consolidation of soft clay which can allow for these two factors simultaneously is proposed. Utilizing the finite difference method, the numerical model for this problem is developed. With the numerical model, the effects of the geometrical nonlinearity and the non-Darcian flow on the consolidation of the soft soil are investigated. The results show that when the self-weight stress is calculated by the same method, the rate of the non-Darcian consolidation for the large-strain case is larger than that for the small-strain case, but the difference between them is limited. However, the difference between the consolidation rates caused by the non-Darcian and Darcian flows is significant. Therefore, when the geometrical nonlinearity of the soft clay is considered in calculating the consolidation settlement, due to the complexity of the large-strain assumption, the small-strain assumption can be used to replace it if the self-weight stress for the small-strain assumption is calculated by considering its sedimentation. However, due to the aforementioned large difference between the consolidation rates with consideration of the non-Darcian flow in soft clay or not, it is better to consider the non-Darcian flow law for both the small and large stain assumptions.