Shield excavation and tail grouting are the main causes of ground deformation in tunnel construction, especially in the case of new tunnels undercrossing existing tunnels, which have stricter requirements for settlement control. This paper investigates the equivalent layer method, which is used to simulate ground deformation induced by shield construction and tail grouting via numerical analysis. The research is based on a case study of Beijing’s newly built Metro Line 12 undercrossing the existing Metro Line 10, which is constructed in soft soil. Three-dimensional finite simulation via Plaxis 3D is performed, incorporating the equivalent layer method. Parametric analysis is carried out to explore the influence of the thickness (δ) and elastic modulus (E) of the equivalent layer on surface settlement. It is shown that the surface settlement increases almost linearly with the increase in δ, and it is insensitive to changes in E. The δ is the dominating factor affecting the surface settlement. Based on the Beijing Metro Lines project, the predicted surface settlement is analyzed and compared with monitoring data. Based on a case study of Beijing Metro, the applicability of the equivalent layer method is verified, and the empirical values for δ and E are summarized. δ = 1.8 Gp and E = 2 MPa are suitable values for analysis, which could be references for other shield tunnel constructions in soft soil. With the obtained empirical values of the equivalent layer method, the deformation caused by grouting and undercrossing tunnels could be accurately predicted, which is benefit for reducing budget and environmental protection.