In　this　work,　CE-LIF　was　employed　to　investigate　the　amino　acid　metabolites　produced　by　Escherichia　coli　(E.　coli)　in　microbial　fuel　cell　(MFC).　Two　peptides,　L-carnosine　and　L-alanyl-glycine,　together　with　six　amino　acids,　cystine,　alanine,　lysine,　methionine,　tyrosine,　arginine　were　separated　and　detected　in　advance　by　a　CE-LIF　system　coupled　with　a　homemade　spontaneous　injection　device.　The　injection　device　was　devised　to　alleviate　the　effect　of　electrical　discrimination　for　analytes　during　sample　injection.　All　analytes　could　be　completely　separated　within　8　min　with　detection　limits　of　20-300　nmol/L.　Then　this　method　was　applied　to　analyze　the　substrate　solution　containing　amino　acid　metabolites　produced　by　E.　coli.　L-carnosine,　L-alanyl-glycine,　and　cystine　were　used　as　the　carbon,　nitrogen,　and　sulfur　source　for　the　E.　coli　culture　in　the　MFC　to　investigate　the　amino　acid　metabolites　during　metabolism.　Two　MFCs　were　used　to　compare　the　activity　of　metabolism　of　the　bacteria.　In　the　sample　collected　at　the　running　time　200　h　of　MFC,　the　amino　acid　methionine　was　discovered　as　the　metabolite　with　the　concentrations　23.3　mu　g/L.