Background Bacillus amyloliquefaciens (BA) and Bacillus subtilis (BS) are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals. However, few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling. If the BA and BS inoculants have positive effects on silages, then they could not only improve fermentation characteristics, but also deliver BA or BS viable cells to ruminants, which would play its probiotic effect. Therefore, the objectives of this study were to investigate the effects of BA and BS on the fermentation, chemical characteristics, bacterial community and their metabolic pathway of whole-plant corn silage. Results Freshly chopped whole-plant corn was inoculated without or with BA and BS, respectively, and ensiled for 1, 3, 7, 14 and 60 d. Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control, and BA inoculation decreased acetic acid concentrations, whereas BS inoculation decreased fiber contents and increased crude protein (CP) content. Higher water-soluble carbohydrate contents and lower starch contents were observed in BA- and BS-inoculated silages compared with that in control. The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage, which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage. In addition, it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins, and decreased the relative abundances of drug resistance: antimicrobial pathways. We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study. There were no significant differences in bacterial community compositions among the three groups during ensiling. However, BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter. Conclusion Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.