The ground surface deformation induced by shield tunnels passing through enclosure structure of existing tunnels is a particular underground construction scenario, which is encountered in Wuhan metro line 12 engineering cases in China. The classic ground deformation theory is difficult to accurately predict this ground deformation. This paper develops a semi-analytical method to predict ground heave considering space effect in this engineering condition. Based on improved ground deformation theory, a novel deformation prediction method of ground and enclosure structure is derived combined with Kirchhoff plate theory. Comparing with field deformation measurements, the maximum difference between measured and calculated deformation is 14.6%, which demonstrating that the proposed method can be used to predict the ground heave induced by shield tunnels passing through the enclosure structure of existing tunnels. The parameters of underground diaphragm wall used in Wuhan metro line 12 are further studied in detail. The results show that the ground heaves have positive correlation with embedded ratio of diaphragm wall, but negative correlation with its elastic modulus and thickness. But the thickness and embedded ratio has a limited effect on ground heaves. This study provides a technical reference for optimization setting of enclosure structure in protecting existing building.