Prefabricated horizontal drains and vacuum preloading have advantages in the consolidation of ultra-soft dredged sludge and soils for maintenance dredging, reclamation, and ground improvement in coastal regions. While laboratory tests and field trial projects have been reported, a convenient analysis and design method is still unavailable. This study proposes a new simple method for the settlement analysis of soft soils considering horizontal drains, vacuum preloading, creep, and large-strain effects. A unified equation is constructed to account for various layouts of horizontal drains in consolidation. A new explicit method is developed to consider the large-strain deformation with the nonlinear evolution of permeability and compressibility of ultra-soft soils under vacuum preloading. The viscous compression is taken into account using a simplified Hypothesis B method. The proposed solution also facilitates convenient consideration of multiple layers of soils and drains subjected to staged loading. The proposed method is examined by a series of physical model tests with different horizontal drain dimensions. Finally, the method is applied in the analysis of two well-documented field cases in Hong Kong and Japan, which confirms its effectiveness and accuracy.