Abstract: A linear programming model was applied to optimize agricultural structure in Taihu lake Basin, not only agricultural economy development, but also agricultural non-point source pollution(ANPSP) and grain and food supply security were taken into consideration. In this model, 72 variables of 6 partitions were set. In this study, optimal scheme of agricultural structure in Taihu lake Basin and its partitions were concluded, which assured an ANPSP reduction rate of 35.1% on the premise of food security guarantee and agricultural output value unchanged. According to the study result, it is suggested that large area of dry land cultivation should be changed into protected cultivation and paddy field and a large amount of pig and poultry breeding should be reduced, while 2/3 or more of freshwater culture should be kept. According to the study results, it is suggested that large area of dry land cultivation should be changed into protected cultivation and paddy field and a large amount of pig and poultry breeding should be reduced, while 2/3 or more of freshwater culture should be kept. At last, different adjusting advices to different partitions are put forward.