One efficient way to manage infections spread by the soil is to sterilize the soil. Currently, chemical fumigation and biofumigation are the commonly used soil disinfection techniques. However, few research has been done comparing and contrasting the impacts of chemical and biofumigation on soil microbial populations. In this study, unfumigated soil was used as a control, and 0.1%, 0.2% and 0.5% (mass fraction) Brassica juncea seed meals and 0.1% (mass fraction) metam-sodium were added to the soil to investigate the changes in soil microbial communities and the differences between them under Brassica juncea seed meals fumigation and metam-sodium fumigation. The results showed that there were both similarities and differences in the effects of Brassica juncea seed meals fumigation and metam-sodium fumigation on soil microbial communities. Brassica juncea seed meals fumigation and metham-sodium fumigation significantly altered the structures of soil bacterial and fungal communities (P<0.01). The type and the amount of fumigant materials, rather than the duration of the fumigation, significantly affected the structure of soil bacterial and fungal communities (P<0.01). In terms of sterilizing harmful microorganisms, the 0.5% (mass fraction) Brassica juncea seed meals fumigation and metam-sodium fumigation reduced the relative abundance of Fusarium in the soil. In terms of enriching beneficial microorganisms, Brassica juncea seed meals fumigation and metham-sodium fumigation were able to enrich Bacillus and Actinomadura. The 0.5% (mass fraction) Brassica juncea seed meals fumigation were able to enrich Luteimonas and Nonomuraea. Metham-sodium fumigation could enrich Micromonospora. In terms of microbial function, the 0.5% (mass fraction) Brassica juncea seed meals fumigation and metham-sodium fumigation were capable of enhancing the bacterial functions of chemoheterotrophy and aerobic chemoheterotrophy and weaken the soil fungal disease-related functions. In conclusion, Brassica juncea seed meals fumigation and metham-sodium fumigation could regulate the soil microbial community by enriching the beneficial microorganisms such as Bacillus and Actinomadura and reducing the harmful microorganisms Fusarium, so that the soil could potentially prevent soil-borne fungal diseases and encourage the crop growth.