[Objective] We analyzed the Sigma54 mutant regulon data of Bacillus thuringiensis (Bt) HD73 strain and CcpA mutant regulon data of Bacillus cereus ATCC 14579 strain, and verified the binding of promoter and CcpA protein, to determine Sigma54 and CcpA co-regulated genes in Bt HD73 and enrich the understanding of microbial metabolic regulation network. [Methods] Based on the results of transcriptome sequencing, genes regulated by Sigma54 and CcpA were found via the comparison of homology gene in Bt HD73 strain. cre sequence of promoter was found by blast and verified the binding with CcpA protein by electrophoresis mobility shift assays. [Results] Thirty-one genes were co-regulated by Sigma54 and CcpA in Bt HD73 strain. The fourteen promoters of these genes contained the cre sequence, which could bind to the CcpA protein in vitro. [Conclusion] Fourteen genes were directly regulated by CcpA in Bt HD73, while their transcription was controlled by Sigma 54. This finding provides clues to the study of sporulation and crystalformation through the point of view the metabolic regulation, and enriches the Bt metabolic regulation network.