The long-term consolidation settlement of soft soils under infrastructures is seriously concerned in coastal areas. In practice, soft soil ground is usually composed of multiple layers with different properties, and the effect of soil creep is nonnegligible. However, in conventional consolidation analysis, creep is seldom included during the “primary” consolidation. With conventional creep model, creep strain will reach infinity with time, which is unreasonable in the long-term view. In this study, a new simplified method based on Hypothesis B is presented to calculate both short-term and long-term consolidation settlements of multi-layered soils exhibiting non-linear creep. There are three main characteristics for this new simplified method:(a) the consolidation analysis for multi-layered soil is conducted using spectral method;(b) a nonlinear creep function with creep limit is incorporated to calculate both short-term and long-term creep settlements;(c) the “primary” consolidation and creep are calculated independently and combined with an empirical parameter α together with the consolidation degree U for correcting the creep settlement. Finite element analysis with a self-developed Elastic Visco-Plastic (EVP) constitutive model considering creep limit was also carried out. Verifications by field cases and finite element simulation demonstrate the efficiency and accuracy of the new simplified method in calculating the long-term settlements of soft soil ground under varied engineering conditions. Influences of major parameters selection in the calculation of the new simplified method are also discussed.