This study aimed to investigate the effects of fermented milk co-fermented with Lactobacillus (L.) helveticus and commercial starter during storage. Thus, systematic analysis revealed the changes with the determination of physicochemical characteristics, functional properties, and metabolome of fermented milk produced by commercial starter Mild 1.0, L. helveticus H11 (H11), and their combination. Co-fermentation with H11 significantly reduced fermentation time and enhanced pH, titratable acidity, viscosity, water-holding capacity, viable counts of H11, sensory attributes, angiotensin-converting enzyme inhibitory activity, valine-proline-proline and isoleucine-proline-proline levels, and storage stability. Additionally, co-fermentation with H11 enriched seven specific flavor compounds (5-tricosyl-1,3-benzenediol, didodecyl thiobispropanoate, glabrone, tuberoside, isomangiferin, indole-5,6-quinone, and luteone 7-glucoside) and five functional metabolites (indolelactic acid, glycine-histidine, stachyose, riboflavin, and asparagusic acid). These findings established H11 as a valuable adjunct culture for the application of commercial starter to produce functional fermented dairy products.