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During malolactic fermentation (MLF) of vinification, the harsh L–malic acid undergoes transformation into the milder L–lactic acid, and via decarboxylation reactions it is catalyzed by malolactic enzymes in LAB. The use of bacterial malolactic starter cultures, which usually present challenges in the industry as the suboptimal conditions after alcoholic fermentation (AF), including nutrient limitations, low temperatures, acidic pH levels, elevated alcohol, and sulfur dioxide concentrations after AF, lead to “stuck” or “sluggish” MLF and spoilage of wines. <i>Saccharomyces uvarum</i> has interesting oenological properties and provides a stronger aromatic intensity than <i>Saccharomyces cerevisiae</i> in AF. In the study, the biological pathways of deacidification were constructed in <i>S. uvarum</i>, which made the <i>S. uvarum</i> carry out the AF and MLF simultaneously, as different genes encoding malolactic enzyme (<i>mleS</i> or <i>mleA</i>), malic enzyme (<i>MAE2</i>), and malate permease (<i>melP</i> or <i>MAE1</i>) from <i>Schizosaccharomyces pombe</i>, <i>Lactococcus lactis</i>, <i>Oenococcus oeni</i>, and <i>Lactobacillus plantarum</i> were heterologously expressed. For further inquiry, the effect of L–malic acid metabolism on the flavor balance in wine, the related flavor substances, higher alcohols, and esters production, were detected. Of all the recombinants, the strains WYm1S_N with coexpression of malate permease gene <i>MAE1</i> from <i>S. pombe</i> and malolactic enzyme gene <i>mleS</i> from <i>L. lactis</i> and WYm1m2 with coexpression of gene <i>MAE1</i> and malate permease gene <i>MAE2</i> from <i>S. pombe</i> could reduce the L–malic acid contents to about 1 g/L, and in which the mutant WYm1S_N exhibited the best effect on the flavor quality improvement.