Stone columns are commonly used in the treatment of soft foundations. However, there is a lack of quantitative research focused on their shear strength characteristics, which limits their ability to meet actual engineering needs. This study investigates the shear strength characteristics of stone column composite foundations using physical model tests and numerical experiments as the main technical methods. The following conclusions were drawn: 1) Three groups of simple shear model tests were conducted with a stone column replacement rate of 19.6% under unconsolidated, unconsolidated with flexible permeable membrane wrapped stone columns, and consolidated conditions respectively. Compared with the original soft foundation, the shear strengths of the composite foundations were significantly improved. The first two schemes showed very similar shear strength, while the consolidated scheme exhibited further improvement. This suggests that the flexible constraint of soft soil around the stone columns can enhance the overall shear characteristics of the composite foundation. The shear strength of the composite foundation was closely related to the significant improvement of permeability performance. 2) Another group of unconsolidated shear tests was conducted after increasing the replacement rate of stone columns from 19.6% to 24.5%. Compared with the consolidated shear test under a 19.6% replacement rate, the difference in shear strength was not significant. This indicates that promoting consolidation can be a more economical and effective way of improving the shear strength of the composite foundation at relatively low replacement rates. 3) Numerical shear tests of stone column composite foundations were carried out. The shear strength parameters of soil in different consolidation and drainage states were selected as the main control factor. Compared with the shear strength parameters of soil in the corresponding consolidated and drainage states, the feedback shear strength parameters of soil around columns in physical simple shear tests were improved. This verifies that stone columns significantly improve the consolidated and drainage environment of natural foundations. Overall, this study provides valuable insights into the shear strength characteristics of stone column composite foundations and proposes effective methods of improving their performance in practical applications.