Carotenoids are a class of terpenes of commercial interest and exert important biological functions. Engineering morphological and biosynthetic aspects of Escherichia coli cell membrane could improve its storage capacity for β-carotene. However, how the synthesis of phosphatidylethanolamine, the major component of the cell membrane, was not discussed in detail. In this work, the synthesis of phosphatidylethanolamine was divided into three modules to discuss their synergetic effect, by expressing in different combinations. Overexpressing the upstream module 1 in CAR016 caused a 30.5% increase of β-carotene specific production (from 10.1 mg/g to 13.7 mg/g DCW); combined overexpressing module 1 and module 2 in CAR016 led to a 122% increase of β-carotene specific production (from 10.5 mg/g to 22.3 mg/g DCW). The optimal expression combination of the phosphatidylethanolamine synthetic pathway was obtained, which further increased the content of the cell membrane for β-carotene storage, and improved its production. The membrane engineering strategy opens up a new direction for engineering microbial producers for a large spectrum of hydrophobic molecules.