Disclosed are a composition and system for separating and detecting an alpha-fetoprotein variant, comprising a separation reagent and a detection reagent; a system for separating and detecting an alpha-fetoprotein variant and a use thereof; and a kit for separating and detecting the alpha-fetoprotein variant. By means of the composition and system for separating and detecting the alpha-fetoprotein variant, and the use thereof, primary liver cancer can be indicated early on, the sensitivity is high, and the method is rapid, simple and automated.