Three damaging soybean diseases, Sclerotinia stem rot caused by a fungus Sclerotinia sclerotiorum (Lid.) de Bary, Phytophthora root rot caused by a fungus Phytophthora sojae, and soybean cyst nematode (Heterodera glycines Ichinohe), are destructive to soybean growth and yield and cause huge economic losses. Biocontrol is an effective way to control soybean diseases with the advantage of being environmentally friendly and sustainable. To date, few reviews have reported the control of these three soybean diseases through biocontrol measures. In this review, the biological characteristics of the three pathogens and the incidence features of the three soybean diseases were first introduced. Then, biocontrol agents containing fungi and bacteria capable of controlling the three diseases, as well as their control abilities, were emphasized, followed by their mechanisms of biocontrol action. Bacillus and Streptomyces were found to possess the ability to control all three soybean diseases under greenhouse or field conditions. Finally, suggestions about screening new biocontrol species and deeply studied biocontrol molecular mechanisms are provided for further research on the biocontrol of soybean diseases.