It is of importance but great difficulty to objectively and quantitatively evaluate the sustainable development level, especially in the weight determination process and uncertainty evaluation. The traditional weight determination methods hardly reflect the coupling effect (interaction) among the indices. More importantly, conventional evaluation methods seldom consider the uncertainties of the indices in the index system. Thus, it is indispensable to apply a more comprehensive approach to solve these defects. This paper presents a new method to evaluate the sustainable development level. The approach integrates the advantages of the Extended Fourier Amplitude Sensitivity Test (EFAST) and Set Pair Analysis (SPA) (called EFAST-SPA). The EFAST algorithm is used to determine the indices’ weight, and the SPA is employed to handle the uncertain relations in the evaluation system and to calculate the sustainable development level. A quantitative evaluation on the agricultural sustainable development in the middle reaches of Heihe river has been conducted using the EFAST-SPA method. The results have been compared with the traditional entropy method and it was concluded that EFAST-SPA and entropy are highly in line with the actual development status. In most cases, the EFAST-SPA method can describe the development levels more accurately, which reflects a higher reliability and application value of this proposed approach. Moreover, the presented method deepens the understanding of sustainable development evaluation from the view of uncertainty analysis inside the evaluation system.