Based on the fact of insufficient agglomeration in the industrialization of the rural economy, this paper uses the theory of the urban agglomerate economy to analyze the agglomeration effects of industrial activities in the urban and its peripheral areas. By Introducing the constraint condition of the segregation of rural and urban economy, we find that the segregation leads to the duality of agglomeration and that the level and effects of agglomeration differ in rural and urban areas as well as in different regions .The results also suggest that an enhancement in agglomeration level in the periphery can increase the productivities , which implies attention should not only be paid to the overall economy development, but also more to promote the integration of the rural and urban economy in order to enhance the level of agglomeration and diminish gaps between regions and rural-urban areas.