In heritage protection research, much attention has been paid to community value perception and decision making. Agricultural heritage systems are living heritages and a special kind of protected area managed and conserved by local farmers as the main actor. Farmers’ cognition of the value of heritage can impact their initiative of conservation and the sustainability of the systems. Their value judgment of the heritage also matters to their cultural self-consciousness and reflects conservation effects. This research proposed a contingent valuation method (CVM) based approach to reflect farmers’ value judgement revealed by rural households’ willingness to pay (WTP) for conservation and its influencing factors. This method was tested with the Globally Important Agricultural System (GIAHS) of Xinghua Duotian Agrosystem. The case study showed that (1) the positive willingness to pay was merely 43.2%, and household economic conditions and the perception of heritages had significant effects on rural households’ positive/negative willingness to pay and the choice of payment, respectively; (2) 61.6% of the non-payment respondents regarded heritage conservation a government responsibility; (3) rural households’ perception of heritages scored low with a limited cultural self-consciousness and lack of benefit from conservation. These results revealed that the farmers’ cognition of the heritage value and participation in conservation were still limited although much had been achieved during the protection and development in the heritage site. Therefore, it is necessary to rethink the role of conservation main actors and the way to conserve, so that rural households can have a better understanding of various values of the GIAHS and actively participate in conserving the dynamic and living heritages. This proposed approach was found feasible in studying community value perception and conservation effect. Considering similar rural development issues in protected areas and national park pilots, this research may provide a useful view and method to study community co-management in protected areas.