Food security is a top priority for a country. Grain processing enterprises are an important part of ensuring food security, the micro-foundation of structural reform on the agricultural supply side, and an important component of achieving agricultural modernization. The research group visited 176 grain processing enterprises of different scales in 17 provinces of China, collected detailed data on the production and operation of enterprises from 2013 to 2016, and processed the data using scientific methods to obtain 704 pieces of data reflecting the production and operation status of grain processing enterprises, including financial costs, labor costs, daily processing capacity, and daily processing capacity. All the data formed a cost-benefit dataset for grain processing enterprises in China from 2013 to 2016. The dataset provides the possibility for research on grain processing capacity, assists in conducting research on the cost-benefit of grain processing enterprises, and supports decision-making by the government and relevant departments.