The value of agro-ecosystem services is closely related to crop yield. As a production input component in an agro-ecosystem, agro-ecosystem services have practical value. It is generally believed that agroecosystem services are substitutes for purchase investment and can decrease agricultural production costs. Crop yield increases may negatively affect agro-ecosystem protection, and conversely, agroecosystem protection may result in crop yield reductions. Based on the established production model of agro-ecosystems, we determined the reasonable substitutive conditions and production outputs, and we quantitatively studied the ratio of the land area for agricultural production to that for ecosystem services. With the upper Yongding River Basin in China as the study area, we calculated agricultural yield elasticity and concluded that the corresponding crop yield would be reduced by 2.7% when the land area for ecosystem services in the basin increased by 1.0%. At present, the ecological service value of the Yongding River Basin showed an increasing trend.