Abstract: As environmental issues have become increasingly prominent in rural development, researches on investment in different agricultural systems and the transformation processes of agricultural products are critical in resolving non-point source pollution issues of rural environment. They also contribute to the development of targeted programs for controlling non-point source pollution. In this paper, the PRA (Participatory Rural Appraisal) method was used to assess fertilizer input of different modes of management of agriculture in the Three Gorges Reservoir Area of Chongqing. Based on the investigated materials and the results of comprehensive assessment of the research area, agricultural production and operation modes were divided into general farmers (GF), big farming households (BF), company enterprises (CE), big breeding households (BB), big farming and breeding households (FB) and co-operative farmers (CF). By accounting for fertilizer input per unit land area in different agricultural operation modes, the distinct variation characteristics of the quantity and structure of fertilizers were identified in the research area. The results showed that: 1) The total amount of fertilizer consumption increased from 1997 to 2011, while the total amount of compound fertilizer grew significantly in recent years. 2) Although different agricultural operation modes had different structures of fertilizers, there were some internal similarities existed among GF, BB and FB and also among BF, CE and CP. While GF, BB and FB farmers used large proportions of conventional fertilizers, BF, CE and CP farmers used more emerging fertilizers like organic fertilizer, K fertilizers, etc. 3) The structures of fertilizer in the research area were dominated by conventional fertilizers, with significantly higher N and P input per unit land area under GF and BF than under CE, BB, FB and CP. 4) The variations in planting structures were due to variations in agricultural operation modes. GF, BB, and FB modes were mainly of traditional crops like corn, rice, sweet potato and irish potato, showing a small but comprehensive characteristics. While BF, CE and CP had the great breakthrough in terms of technological support, commercial production operations in some areas turned to the production of distinct crops. The order of fertilizer input per unit land area for different corps of the agricultural operating modes in the Three Gorges Reservoir Area of Chongqing was corn > vegetables > potatoes > other crops > sweet potatoes > fruit garden > paddy.