Rapid and efficient inactivation of the target gene on Escherichia coli chromosome is the precondition and groundwork of researches on metabolic engineering. In the present study, we demonstrated a multiple gene inactivation approach in E. coli mediated by Red recombination and Xer recombination. The chromosomal genes, ackA-pta and pps, in a wild type strain E. coli CICIM B0013 were inactivated by this method indicating that dif sites can be reused to inactivate multiple chromosomal genes with no antibiotic resistance selectable marker remain. Furthermore, this method has high recombination efficiency and simplified steps.