The secondary salinized soil in greenhouse often contains excessive nitrate. The inoculation of Bacillus megaterium NCT-2 with nitrate assimilation ability seems to be attractive in remediation of secondary salinized soil. However, the effects of NCT-2 inoculant on the structure and function of microbial community have not been explored. In the present study, greenhouse experiments were carried out to investigate the responses of soil properties, Brassica chinensis L. growth, bacterial and fungal community to the NCT-2 inoculation. Results showed that the NCT-2 inoculant has stronger reduction ability of nitrate than other salt ions. It also significantly reduced the nitrate content in B. chinensis. Moreover, the perturbation of NCT-2 to the structure and function of bacterial community is negligible. While the NCT-2 inoculant resulted in a larger disturbance to both the structure and function of fungal community in soil. Especially, its strong inhibitory effect on ectomycorrhizal fungi lasted until the end of experiment. However, at the end, the soil with NCT-2 inoculation showed similar structure and function of microbial community to the control. Therefore, the NCT-2 inoculant caused a low disturbance of indigenous microbial community in soil on the whole. The present study will improve understanding of microbial interaction in response to bacterial inoculation and can be of great significance for the application of NCT-2 inoculant in remediation of secondary salinized soil.