Through pot experiment, this paper studied the effect of two soil-treated herbicides on 34 different millet cultivars. By using clustering analysis, we can compare the difference between the different millet cultivars′ herbicide resistance after measuring the physiological indicators. The experiment results indicated that, different herbicides could inhibit the plant height and leaf surface area of most millet cultivars. Prometryn(0.07g/m2) increased most cultivars′POD, their soluble sugar level，their evaporation rates and the conductibility of their stomata. Flumioxazin(fmx)(0.015g/m2) decreased most cultivars’ SOD, their evaporation rates and increased the conductibility of their stomata. The same herbicide had different effects on the physiological indicators of the different millet cultivars. By the cluster analysis of 34 millet cultivars was classified into 4 groups, the results showed that different millet cultivar had different tolerance on herbicides.