Water storage of the Three Gorges Project (TGP), immigration resettlement and changes of land use pattern may have long-term potential impacts on soil fertility, land productivity and agricultural production development in the head part area of the Three Gorges Reservoir (TGR). Based on these backgrounds, 85 soil samples of three typical land use patterns (farmland, orchard and tea garden) in the rural regions of Ziui, Xingshan and Badong counties were analyzed, and local land productivity and economic status in the head part of the TGR were also investigated. The results were as follow: After water storage of the TGP, The fertility of farmland soil was relatively high, followed by orchard soil, but tea garden soil was relatively low; To meet the demand for development of agricultural production, local agricultural input increased, especially fertilizer input into orchard and tea garden; Yield and per unit area yield of grain decreased during water storage of the TGP and immigration resettlement, especially in Zuigui country, but grain production in the head part area of the TGR kept steady; Planting areas and yields of citrus and vegetable in three counties in the head part area of the TGR increased year by year, superior industries and land productivities were not impacted significantly; Economic benefit of citrus industry was significant higher than those of tea and crop, per capita net incomes of Zigui and Xingshan countries increased year by year, economic level in the head part area of the TGR kept steady growth.