Soybean fungal root rot diseases are the most serious soybean disease problem in Heilongjiang province. The microbial seed dressing agent comprised of Bacillus strain B29 which showed strong antagonistic ability to the pathogens of Fusarium oxysporum, Pythium spp. and Rhizoctonia solani were applied to control soybean fungal root rot in field. The control efficiencies of the treatment T3, T4, T5, T6 on soybean fungal root rot after 35-day cultivation were 50.2%, 60.0%, 48.3%, 49.4% respectively, which were better than that of Carbendazim-Carbofuran-Thiram seed coating agent (T2). The second investigation after 50-day cultivation showed the control efficiency of T4 was the best (60.7%), while the control efficiency of T3 was not significantly different from T2. The control efficiencies of T5 and T6 were lower than that of T2. The microbial seed dressing agents were safe to soybean cultivation based on the investigation on seed germination rate, plant height, fresh weight and root nodules. The results based on 2-year demonstrating in field showed that soybean seeds germinating rate was more than 90% after seeds dressing by the microbial seed dressing agents, and the control efficiencies on soybean root rot diseases were 56.3% to 89.1%. It suggested that the microbial seed dressing agents were not only efficient to control soybean root rot diseases but also increased soybean productions.