Since the government launched the open-door policy in 1978, China has been experiencing a gradual transition from command economy to a market economy, and has achieved tremendous economic growth in the last three decades. In the 21st century, reclamation area enters a period of rapid economic growth fueled by the agricultural modernization, urbanization, industrialization and farm-county cooperation. Based on the Gini coefficient, this paper examined the changing characteristics of regional economic disparity of the reclamation area in Sanjiang Plain, and explained the influence of industrial factors by the structural effect, concentrated effect and comprehensive effect of the Gini coefficient, and then discussed the spatial association of economic inequality and industrial structure using the gray correlation model. The results are shown as follows. Firstly, the economic disparity takes on an obvious trend from decline to ascension since 2000. The gap of the primary industry among regions accounts for the majority contribution to economic inequality, and the inner difference of per capita agricultural resources is an important basis. Secondly, there is a close relationship between the change of industrial concentration and regional economic disparity, and the concentrated effect of industrial Gini coefficient change is the main driving force that causes the economic disparity change. Finally, the economic development in reclamation area has a close relationship to agricultural development, and the economic development of most farms relies on the improvement of the ability of comprehensive agriculture production, only a few farms take on the tendency of non-agriculturalization.