It is normal to increase grain production by applying large quantity of fertilizer in China. Based on provincial level cost-benefit survey data of agricultural products from 2004 to 2013, this paper evaluated the over fertilization phenomena in the production of wheat, rice, and corn in China and also empirically analyzed the influencing factors of over fertilization. Results show that from the economic perspective, the fertilization quantity has passed the economic optimal level for all these three crops in China. Among them, corn producers are overusing fertilizer by up to 50.74%, wheat producers by up to 27.26%, and rice producers by up to 24.67%. Migration of rural labors, disaster area ratio, crop prices of previous year and the current extension service system have significant positive influences on the magnitude of over fertilization; while properly expansion of management scale does help to relieve this phenomenon. To decrease fertilizer application, this paper provides the following suggestions: improving fertilizer application technology, moderately intervening agricultural labor force transfer, reforming the current agricultural extension system, and developing and promoting agricultural insurance to increase farmers’ risk resistance capacity.