This study investigated the biofumigation effects of Brassica juncea crop on soil nitrification and soil bacterial communities under gray lowland soil conditions. Treatments included incorporating B. juncea containing high levels of glucosinolate (GLS) or Sinapis alba containing low levels of GLS and unamended control. Nitrification activity was evaluated using soils collected at the sweet corn transplantation (8 days after incorporation) and tassel emergence stage (46 days after incorporation). Sweet corn growth, yield, and nitrogen status were compared among treatments. Additionally, soil bacterial community structure in initial soils and soils at maize transplantation were investigated using next-generation sequencing. The results showed that incorporating B. juncea plants did not inhibit soil nitrification at the transplanting and tassel emergence stages, and apparent differences in sweet corn yield and nitrogen uptake were not observed among treatments. Differences between treatments regarding the effects of the incorporation on the soil bacterial abundance were observed in some bacterial families, but the abundances of nitrifying bacteria were not statistically different. Our results showed that incorporating B. juncea, which has a high GLS content, into sweet corn cultivation soil changed the abundance of certain soil bacterial families; however, nitrification inhibition effect is not expected under gray lowland soil conditions.