Dual health social security institution exist independently in urban and rural area in Pudong New Area, as a result of both different health systems and uneven distribution of health resources between rural and urban area.In rural area, the dominant one is the cooperative health security system.And its security level is lower than that in urban area, which is comparatively perfect.With the urbanization process, the dual systems are not suitable for the urban-rural integrated socio-economic development in Pudong New Area.The paper provides the strategic development of the integration of the dual systems, which is based on the institutional innovation, so as for a successful transformation from the dual structure to an integrated one.