The deformation pattern of the stratum caused by constructing a new metro tunnel crossing an existing tunnel is different from the deformation pattern caused by general tunnel construction. However, the prediction results by the ordinary surface settlement prediction model often bring significant errors because the complex influence of existing tunnels on the surface settlement caused by the excavation of new tunnels is always neglected. Based on the equivalent layered method and stochastic medium theory, a prediction model for the surface settlement due to excavating a new tunnel under an existing tunnel in the heterogeneous stratum was established. By equating the bending stiffness of an existing tunnel before and after applying the equivalent layered method, the layer index was determined. The critical parameters of the stochastic medium theory were derived based on the relationship between the critical parameters of both the Peck empirical formula and the stochastic medium theory. The surface settlement of some typical projects was predicted and compared by the prediction model in this paper and the ordinary prediction model. The comparison shows that the proposed prediction model and parameter determination method in this paper had high accuracy and applicability. The results of the prediction model in this paper fit the results of numerical calculation. The research of this paper can provide a new method for the theoretical prediction of surface settlement caused by the excavation of a new tunnel under an existing tunnel in the heterogeneous stratum and the determination of critical parameters of the stochastic medium theory.problem in the construction industry, and helps reducing the material waste and budget cost.