Abundant practical evidences have indicated that the soil progressively loses its structural configuration under construction disturbance and this can result in long-term macro deformation. The fundamental understanding of soil microstructure evolution subject to construction disturbance is necessary for controlling disturbance in excavation projects and minimizing ground settlement. The microstructure of Shanghai soft soil is investigated in this study. The laboratory isotropic compression tests are respectively performed on the virgin soil and the reconstructed Shanghai soft soil to investigate the macro deformation of soil under disturbance. Discrete element method model is used to study the micro particle level responses of soil under disturbance. The laboratory tests and numerical simulations provide theoretical basis for construction disturbance mitigation to ensure safety and stability of excavation projects. © 2016, Shanghai Jiaotong University and Springer-Verlag Berlin Heidelberg.