This paper presents a method of analyzing efficiency of tobacco automated sorting system and two optimal methods based on the results of analysis.In efficiency analysis, we create a definition-efficiency bottleneck as the criterion of efficiency judgement. Then based on bottleneck, we devise 2 kinds of optimal methods. One mends the system's sorting algorithm to fit the bottleneck; the other eliminates the bottleneck radically by changing the layout of sorting system. The first method improves system's sorting efficiency from 7500/h to 9500/h, while the second method can improve system's sorting efficiency above 12000/h.