Numerical analysis is widely used to study the excavation deformation of deep foundation pits in complex environment, but the constitutive model and the selection of model parameters have great influence on the rationality of calculation results. By comparing and analyzing the characteristics of various constitutive models, it is found that the constitutive model of hardening soil with small strain (HSS) can well predict the deformation caused by excavation of foundation pit in soft soil sites, but the parameters of HSS model are difficult to take values. The lacustrine sedimentary soft soil is widely distributed in Kunming area, but there are no relevant studies on how to select the parameters of HSS model for such soil, especially peaty soil with high organic matter content and water content. To solve these problems, data of many geotechnical tests and indoor tests of undisturbed samples were analyzed, and the relationship among empirical values of several stiffness parameters were obtained, then the HSS model parameters of typical lacustrine sedimentary soft soil were obtained. To examine the rationality of HSS model and related parameter values, numerical models for two subway foundation pits in soft soil site were established using the numerical analysis software PLAXIS 2D. The deformation of foundation pits under different excavation conditions were calculate and compared with the monitoring value of actual deformation. Results show that they are in good agreement, indicating that the calculated results are reasonable and reliable. The research results have important reference value for the support design of deep foundation pit and the geotechnical engineering research and investigation.