[Objective] The nitrogen fixation (nif) gene operon (nifBHDKEfNXhesAnifV) of Paenibacillus polymyxa WLY78 encoding the nitrogenase enabled Escherichia coli to synthesize functional nitrogenase. The genome-wide transcriptional profiling of the recombinant E. coli 78-7 was examined for improving its nitrogenase activity. [Methods] The transcriptomic analysis of the recombinant E. coli 78-7 cultured under non-N₂-fixing (air and 100 mmol/L NH₄⁺) and N₂-fixing (without O₂ and NH₄⁺) conditions was implemented. [Results] These results reveal that nif genes were significantly transcribed under both conditions, indicating that the negative regulation of nif gene transcription by O₂ and NH₄⁺ is bypassed in heterogeneous E. coli. The non-nif genes specifically required for nitrogen fixation, such as mod, cys and feoAB encoding transporters of Mo, S, Fe and electron transporters, respectively, were transcribed at different levels in both conditions. The transcription levels of suf operon and isc system specific for the synthesis of the Fe-S cluster varied greatly. The genes involved in nitrogen metabolism were notably up-regulated in N₂-fixing conditions.[Conclusion] These data suggest that the non-nif genes specifically required for nitrogen fixation in recombinant E. coli had obvious effects on its expression of nitrogenase. Our results will provide valuable exploration regarding the improvement for nitrogenase activity of heterogeneous hosts.