In water governance, the government, downstream residents, and upstream farmers are closely associated stakeholders. The participation willingness of upstream farmers directly bears on the success of environmental policies. Xin’an River Reservoir Water Protection Zone is the second water source region of Hangzhou, China. Taking this region, for example, this paper surveys the willingness to accept compensation of local rice farmers, mainly using Choice Modelling (CM) methodology. This paper assesses the farmers’ willingness of minimum compensation amount to adopt various ecological compensation means and, on this basis, discusses the key factors determining their willingness to accept compensation. It helps to confirm that the farmer participation mainly depends on whether the government could provide satisfactory compensation incentives to cover farmers’ losses. Hence, at the ending of the paper, we call for the relevant departments of the government fully understanding the farmers’ willingness to accept compensation before formulating compensation policies, so that the compensation at least reaches the minimum requirements of farmers. Only in this way could the water source region achieve the optimal efficiency in environmental governance.