On the basis of new characteristics and trend of China’s agricultural development in the post-WTO period, combining analysis of factors influencing agricultural industrial safety, this paper builds an evaluation indicator system for China’s agricultural industrial safety by scientific indicator system design method. This indicator system includes risk factor indicators (showing risk degree) and capacity factor indicators (showing guaranteeing ability), and consists of 7 subsystems: consumption safety, production safety, industrial controlling capacity, industrial development capacity, industrial development environment, government functions and industrial foundation condition. Risk factor is divided into 5 levels: higher risk, high risk, medium risk, low risk and lower risk; guarantee risk is also divided into five levels: strong, healthy, normal, weak and disabled. According to the overall evaluation score obtained from weighting sum, the agricultural industrial safety includes 5 types: very safe, safe, basically safe, not safe and hazardous. This evaluation indicator system is expected to providing theoretical reference for evaluating China’s agricultural industrial safety.