Consolidation and settlement of soft soil ground are the main problems encountered for geotechnical engineers, and drainage boundary conditions play a crucial role in consolidation analysis and settlement prediction. Despite some theoretical approaches that have been proposed incorporating some particular drainage boundary conditions, there remains a dearth of rigorous analytical solutions for multilayered soils that effectively capture various drainage boundary conditions. This study presents a novel approach where the spectral method is used to capture the impact that drainage boundary condition has on the consolidation of multilayered soil. The drainage boundary condition over time is considered, while the excess pore water pressure (EPWP) profile across different soil layers can be described as a single expression using matrix operations. This proposed method is then verified with field investigations where the varying drainage condition is captured and compared with other solutions. The results show that the consolidation behavior will be overestimated if the traditional boundary conditions are used and the proposed method can predict the consolidation of soil with greater accuracy and flexibility. EPWP and settlement at different depths can be estimated such that they agree better with the field data, and the study also indicates that there is a noticeable discrepancy in the predicted consolidation when the drainage boundary condition is not considered properly.