Lipopolysaccharides, the major molecules in the outer membrane of Escherichia coli, affect the behavior of bacteria including outer membrane permeability, but its influence on lycopene production in E. coil has never been reported. In this study, the effects of lipopolysaccharides with different structures on lycopene biosynthesis were investigated. Firstly, the heterogenous crtEBI operon were overexpressed in 10 LPS mutant strains of E. coil W3110 (Delta waaC, Delta waaF, Delta waaY, Delta waaG, Delta waaR, Delta waaO, Delta waaU, Delta waaP, Delta waaY and Delta waaB), and their ability to produce lycopene were compared. Delta waaC/pWSK29-crtEBI, Delta waaF/pWSK29-crtEBI and Delta waaY/pWSK29-crtEBI produced 4.19, 4.20, and 3.81 mg/g lycopene, respectively, while the control W3110/pWSK29-crtEBI produced 3.71 mg/g lycopene; the other strains produced less lycopene than the control. In order to enhance lycopene production, genes dxr, dxr, ispA, and idi were overexpressed in Delta waaC/pWSK29-crtEBI, Delta waaF/pWSK29-crtEBI individually or in combination, and the lycopene production in each strain was analyzed. The maximum yield of 5.39 mg/g was achieved in Delta waaC/pWSK29-crtEBI-SRA, which is 142% higher than that in W3110/pWSK29-crtEBI. The results indicate that the length of lipopolysaccharide affects lycopene biosynthesis in E. con, and the shorter lipopolysaccharide and higher outer membrane permeability might be beneficial to lycopene biosynthesis.