The invention discloses an automatic rhizome peeling and washing assembly line. According to a material processing flow, the assembly line comprises an unpacking platform, a wind remover bubble washer, a cooking machine, a cooling machine, a roller peeling machine, a belt conveyor, a bubble washer and a control cabinet in sequence, wherein the unpacking platform, the wind remover bubble washer, the cooking machine, the cooling machine, the roller peeling machine, the belt conveyor and the bubble washer are connected with the control cabinet. The invention also discloses an automatic rhizome peeling and washing method. The assembly line and the method have the beneficial effects that according to peeling and washing design of rhizomatic Chinese herbal medicine materials and subsidiary agricultural products, the assembly line and the method comprise material washing, material cooking, material cooling, material peeling and secondary washing, are automatic in control of the whole process and satisfy peeling and washing of different materials; and the whole assembly line saves time and labor and is energy-saving and efficient.