The effect of co-fermentation on the quality of yogurt during storage and the underlying mechanism were investigated. With this aim, we monitored changes in some physicochemical properties (pH value, titratable acidity, water-holding capacity and texture properties), and we also analyzed the color, flavor compounds and microstructure of yogurt using a color difference meter, headspace solid phase microextraction-gas chromatography-mass spectrometry and scanning electron microscopy, respectively. The results obtained showed that co-fermentation markedly decreased the pH value, increased the acid production and gelation and enhanced the water-holding capacity and texture properties of yogurt. At the same time, co-fermentation endowed the yogurt with better color and flavor as well as a more compact, continuous, stable structure three-dimensional network structure. To sum up, co-fermentation could significantly improve the quality of fresh and stored yogurt.