Through consultation of literature and field survey, data were collected of the conventional rice, wheat, vegetable and fruit production, the economic benefit of the production under the model of cleaner production and the nitrogen loss in the Zhushanwan catchment, a subwatershed in the northwest of the Taihu Lake Region, and other relevant social-economic data. An attempt was made to readjust the planting structure of the catchment in line with five simulated scenarios (I, II, III, IV and V), separately, high to low in total nitrogen loss, using the linear optimization model (Software Lingo 11) and taking into full account maximal economic benefit and total volume control of pollution discharge. In Scenario Ⅱand Ⅲ, the total N input was found to be 6 267 t and 5 567 t, respectively, and the total N loss 511 t and 447 t, respectively, which indicates that both scenarios meet their respective intended targets of reducing total N input by 20% and total N loss by 30% as compared with that in the conventional planting structure. Besides, the two scenarios may generate a relative net economic profit of 845.6 million yuan and 796.6 million yuan, respectively, both higher than that (787.3 million yuan) the conventional planting structure does. So among the five scenarios, Scenario Ⅱ is the optimal one and Scenario Ⅲ the second to follow for readjustment of the planting structure of the region. The quota of eco-compensation was calculated according to opportunity cost and ecological benefit reward, and the compensation policy and mechanisms were suggested to facilitate implementation of cleaner production. The ecological compensation funds, excluding transaction cost, about 15% of the total compensation for Scenario Ⅱ and Ⅲ is estimated to be 9.61 and 35.07 million yuan (RMB), respectively, according to the standard for compensation, 739 and 2 696 Yuan hm^-2, respectively. Implementation of the policy and its matching eco-compensation measures may effectively help control non-point source agricultural pollution and expedite the process of transformation or escalation of the farming industry in the region from the traditional one to the one of cleaner production.