The invention relates to an aspergillus niger genetic engineering bacterial strain high in yield of malic acid under condition of low pH. The aspergillus niger genetic engineering bacterial strain isprepared through the steps of obtaining a pexG gene knock-out bacterial strain S914; obtaining an expression Malate synthase gene mas* bacterial strain S1016; overexpressing aspergillus niger malic acid transport protein gene dct1, performing transformant screening and hygromycin resistant gene reorganization to obtain an overexpressing dct1 bacterial strain S1140 without a screening mark, namelythe aspergillus niger genetic engineering bacterial strain high in yield of malic acid under condition of low pH. The bacterial strain is based on the natural characteristics that the aspergillus niger resists acid and generates organic acid, through heredity reorganization, the physiological property of the aspergillus niger is reformed, and experiments confirm that the capacity of the aspergillus niger genetic engineering bacterial strain for generating malic acid at low pH can be notably improved. A good strain is provided for preparation of apples by a microbial fermentation method.