The invention discloses a gene engineering bacteria with high-yield malonyl coenzyme A and a construction method and application thereof. The gene engineering bacteria is constructed by: knocking outfive genes (ldhA, pta, frdA, poxB and adhE) in the Escherichia coli genome, and then introducing malonyl coenzyme A synthesis pathway genes including acetyl coenzyme A synthetase gene of the Escherichia coli, acetyl coenzyme A carboxylase gene of Salmonella enteritidis and biotin ligase gene of Corynebacterium glutamicum. According to the gene engineering bacteria of the invention, a highly-efficient accumulation of the malonyl coenzyme A can be realized by inhibiting internal acetyl coenzyme A outflow pathways of the engineering bacteria and constructing malonyl coenzyme A synthesis pathwaysinto different expression vectors to be transferred into the engineering bacteria; the engineering bacteria can efficiently synthesize a precursor, malonyl coenzyme A, of flavonoid compounds by takingacetic acid, a metabolite by-product of the Escherichia coli, as a substrate; and the engineering bacteria can be used to increase the yield of naringenin, a skeleton precursor of the flavonoid compounds, synthesized by a microbiological method.