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The public's stated value and heterogeneous preferences are crucial for formulating policies and financing approaches to promote the control of agricultural non-point-source pollution (ANSP). This study aims to investigate urban residents' willingness to pay (WTP) for ANSP control and analyse the source of preference heterogeneity using a choice experiment method. Survey data were obtained from face-to-face interviews with 595 respondents in south Shaanxi Province, China. We found that respondents' average WTP for the attributes of ANSP control schemes were 2.34 yuan ($0.36) and 5.42 yuan ($0.83) per year per household for a 1% reduction in fertiliser and pesticide use, respectively. We also found significant impacts of WTP from individuals' socio-economic characteristics (i.e., gender, age, education, and income) and cognitive factors (i.e., policy understanding, and government trust). Thus, to improve the efficiency and universality of ANSP control policy, the public's willingness and preference heterogeneity should be thoroughly taken into policy formulation. [Display omitted] • Most urban residents are willing to pay a certain fee for ANSP control. • Public's marginal willingness to pay for the reduction of fertiliser and pesticide 2.34 yuan ($0.36) and 5.42 yuan ($0.83) per year per household for a 1% reduction in fertiliser and pesticide use, respectively. • Reference heterogeneity of urban residents' WTP exists and comes from individuals' socio-economic characteristics and cognitive factors. • When collecting ecological compensation funds from the public, policymakers should fully consider these heterogeneous preferences to formulate adaptive policy and management approaches. [ABSTRACT FROM AUTHOR]