To study the mechanism and efficient alleviation of fluctuation in agricultural system of farming-pastoral transitional zone,fluctuation characteristics of gross grain yield from 1954 to 2013 at Yanchi County in Ningxia Hui Autonomous Region and the regulatory factors were analyzed with stepwise multiple regression,empirical mode decomposition (EMD) and set pair analysis (SPA). The results showed that the gross grain yield in Yanchi County was gradually increased during the past 60 years with the variance contribution at 82.86%. The distinct fluctuation in gross yield of grain accounted for 17.14% of variance. Gross grain yield presented the periodic fluctuation with quasi-periods of 3 a,6 a and 9 a. Magnitude of the 3-year period was the greatest. In addition,the agricultural machinery gross power and irrigable farmland area were two main factors responsible for the gradual increase of gross grain yield. Annual precipitation predominantly regulated 3 a or 6 a quasi-periodic fluctuations of gross grain yield. Grain acreage and fertilizer input rate were the two control factors in short terms. Irrigation water diverted from the Yellow River and effective irrigation area were the negative regulatory factors,showing a significant influence after the occurrence of inflection point became stronger than that before. Furthermore,conversion of agriculture from climate-dependent to hydrology-dependent would be promoted as a result of strengthening the ecological agriculture construction.