Using real-time PCR to detect the effect of supplementing with Malic acid and stearic acid on rumen main functional microbe, including ciliate protozoa, methanogen, cellulolytic bacteria, hydrogenated bacteria and lipolysis bacteria in vitro. The result showed there were significant effect on the quantities of Anaerovibrio lipolytica, which decreased 95.8%(P<0.001), and Fibrobacter succinogenes, which increased 52.5%(P<0.05) after supplemented with Stearic Acid. The quantities of Anaerovibrio lipolytica were decreased by 91.2%(P<0.001) on 5 mmol/L MA group and 94.8%(P<0.001) on 10 mmol/L MA group, and the latter were decreased 41.3%(P<0.05) than the former. The conclusion was stearic acid and malic acid were significantly effected on part of rumen microbe respectively, however, both of them were not obviously effected on them.