By using the statistical data of grain yield in China’s major grain producing areas from 1949 to 2008, and fluctuation theory, the historical process and main cause of fluctuation of grain yield in China’s major grain producing areas are analyzed. The results of research show that the grain yield in China’s major grain producing areas grows in unstable fluctuation, with high-frequency fluctuation cycle and regular length; the amplitude of fluctuation, on the whole, is moderate, with not strong stability; the fluctuation of grain yield has correspondence, reflecting the N-shape developmental trend of grain production at present; the fluctuation of grain yield has gradient characteristics; in the process of comparison of grain yield, the average growth rate annually of grain yield in China’s major grain producing areas is higher than that of the national average, but the relative fluctuation coefficient is also higher than that of the national average. From five aspects, namely natural disaster, agricultural policy, production input, grain price and grain circulation, the cause of fluctuation of grain yield in China’s major grain producing areas is analyzed, and measures of preventing and arresting super-long fluctuation of grain yield are put forward. Firstly, stick to strict farmland protection system, and strive to promote farmland quality; secondly, strengthen infrastructure construction of grain production and beef up the ability of preventing natural disaster; thirdly, quicken the pace of agricultural technology and establish robust technology supporting system; fourthly, lay stress on innovation of agricultural organization system and provide implementation path and vehicle for application of agricultural technology measures; fifthly, perfect disaster precaution system and grain market system, and strengthen the ability of preventing risk of grain production.