The deep excavation of foundation pit in soft soil layer will cause serious disturbance to the soil at the bottom of the pit. Affected by excavation disturbance, the mechanical properties and stress state of the soil at the bottom of the pit will change. Hence, it is important to accurately evaluate the degree of soil disturbance caused by excavation and the influence of disturbance on soil mechanical properties. Based on the summary of the existing evaluation methods of soil disturbance, taking the foundation pit excavation of Taihu tunnel as an example, the distribution of disturbance degree and the depth of strong disturbed zone of soil under the center of the pit bottom under different excavation depths were studied by using the finite element simulation method. Then, taking the undrained shear strength as an evaluation index, a method for evaluating excavation disturbance of clayey soil based on the cone tip resistance in the piezocone penetration test (CPTU) was established. The soil disturbance calculated through cone tip resistance was agreeable with that determined by numerical calculation. Finally, combined with the soil disturbance determined by the finite element method, the settlement of disturbed soil at the bottom of the pit under different base additional stresses was calculated considering the settlement of soil disturbance. The results showed that the soil disturbance would cause a significant increase in the base settlement. When the base additional stress increased from 100 kPa to 150 kPa, the ratio of base settlement with soil disturbance to that without soil disturbance would increase from 1.43 to 2.24.