Based on the field survey data set of households in Mizhi, Ansai and Wuqi in loess hilly regions, this paper introduced the grey relational model and measured the coupling degree of agricultural ecological system. Based on this, the paper further empirically examined the impact of sloping land conversion program (SLCP) on the coupling of agricultural ecological system. The results show that: 1) The coupling of agricultural ecological system in loess hilly regions is in a moderate state, yet not fully achieving the reasonable matching and coordinating situation; 2) SLCP makes a significantly negative effect on the coupling of agricultural ecological system, denoting that the SLCP cannot effectively encourage farmers to adjust their agricultural structure. Therefore the Chinese government should take the effect into consideration when launching a new round of SLCP, and should also mainstream agricultural adaptation to climate change into the SLCP for improving the adaptive capacity of the loess hilly regions. This research is proposed to provide useful inputs for the government's decision making on agricultural development and ecological rehabilitation policy in fragile ecological areas.