The arch aqueduct on pile foundation is formed by beam-column and block structure. The structure should be discretized to beam element and isoparametric element respectively in finite element method analysis. But there is a problem of how to overcome the coordination of corner displacement between beam elements and isoparametric elements. Based on the generalized displacement formula of the beam element node as the master node, the generalized displacement expression between the rotational displacement of the beam element node and the displacement of the embedded isoparametric element node is established. By setting different grid sizes and element stiffness, the applicability of master-slave or slave-master generalized displacement mode between beam element and isoparametric element for structural analysis of arch aqueduct on pile foundation is studied and discussed. The method is also applied to the analysis of an arch aqueduct project. The research results can be popularized to all the interaction problems between beam, slab, column and block structure.