The number of bacteria was dominant over other kinds of microorganisms in all growing stages of soybean in soil, the following soybean was less than that of soybean following other crops, especially in flowering and podding stage. The number of actinomycete doesnt changed evidently, and with soybean following soybean was higher than that of soybean following other crops in flowering and maturing stages, and was opposite in seeding stages. The number of fungi changed obviously, and in soybean following soybean was observed to be much more than that of soybean following other crops, especially in flowering stage. In rhizosphere soil of soybean following soybean, beneficial fungi decreased and pernicious fungi increased. The superior species of fungi, Fusarium oxysporum Schlecht, F.semitectum Berk. et Rav. and Gliocladium roseum (Link) Bain moculated into soybean could produce difference degree pathogenicity and led to soybean root rot, especially in flowering stage (3850 days). It has not been reported that F.semitectum Berk. et Rav. and G.roseum (link) Bain. may result in pathogenicity and soybean root rot. The toxicity experimental results on soybean by the unrefined extract of three fungi toxin manifest were the germination percentage of soybean decreased obviously, and the growth of soybean was hindered.