The present invention relates to recombinant bacteria to which a novel lipid peroxidation system has been applied and a method for preparing a biofuel and a biopolymer using same. The artificial lipid peroxidation system of the present invention can be used to prepare ultra-high concentrations of free fatty acids through artificial lipid peroxidation without cell death, and a biofuel and a biopolymer can be prepared therefrom. In addition, the artificial lipid peroxidation system according to the present invention increases intracellular redox energy density and can thus additionally promote carbon dioxide fixation. Accordingly, it is possible to prepare increased quantities of a biofuel and a biopolymer.