A series of vertical loading tests on stone columns based on transparent soil were conducted to investigate the failure modes and bearing characteristics of stone columns in layered soils. The influences of different layer thicknesses, different layer distributions, and different aggregate gradations on the bearing capacity of stone columns were examined. Based on the experimental results, a bearing capacity calculation method is proposed for stone columns subjected to bulging failures in lower soft soils. This new calculation method incorporates the self-weight of both the column and the surrounding soil. Verification through an engineering case study shows that, compared with the existing calculation methods, the outcomes derived from the proposed approach exhibit superior agreement with field measurements.