Mannose-6-phosphate isomerase encoded by manA gene catalyzes the isomerization of D-mannose and D-fructose in Escherichia coli and promotes the metabolic uptake of carbon sources in Escherichia coli. In this paper， the study of carbon source utilization and gene encoding carbon metabolism in manA mutant strain aims to investigate the effect of mannose-6-phosphate isomerase on the metabolism of Escherichia coli. ManA gene mutant strain was constructed by group II intron reverse transcriptase mutation method. The utilization of manA gene mutant strain on different carbon sources and the effect of manA gene mutant strain on the gene expression of carbon metabolism in Escherichia coli were analyzed. The results showed that the growth of Escherichia coli BL21（DE3）ΔmanA strain was significantly inhibited when the mannose and starch were used as the carbon source， but the growth of BL21（DE3）ΔmanA strain was significantly better than that of wild type strain when starch was used as carbon source. The mutation of manA gene has no significant effect on the growth of BL21（DE3）ΔmanA strain in glucose. Further study gene expression showed that the expression of mannose-related genes in BL21（DE3）ΔmanA strain was significantly decreased. The gene （pfkA） of the 6-phosphoglucose kinase I subunit was significantly down-regulated in the fructose metabolic pathway. The expression of the gene （malS） of the α--amylase of the hydrolyzed starch was up-regulated. In conclusion， The mutation of manA gene affected the gene expression in the mannose， fructose and starch metabolic pathways， thus affecting the utilization of carbon sources in Escherichia coli.