Abstract: In order to explore the effects of lactic acid bacteria on the bioactive substances and in vitro antioxidant capacity of wolfberry yoghurt, Streptococcus thermophilus, Streptococcus thermophilus and Lactobacillus bulgaricus (3:1), Streptococcus thermophilus and Lactobacillus plantarum (1:1), Streptococcus thermophilus and Lactobacillus paracasei (1:1), Streptococcus thermophilus, Lactobacillus bulgaricus and Lactobacillus plantarum (2:1:2), Streptococcus thermophilus, Lactobacillus bulgaricus and Lactobacillus paracasei (2:1:2) were used to prepare wolfberry yoghurt. Results showed that fermentation could increase the content of polyphenols and flavonoids while reducing the content of carotenoids and polysaccharides. Compared to other samples, the wolfberry yogurt sample (SL-Lpc) fermented by Streptococcus thermophilus, Lactobacillus bulgaricus and Lactobacillus paracasei (mixed in a 2:1:2 ratio) exhibited the highest viable bacterial counts. In the SL-Lpc sample, the content of carotenoids and polysaccharides showed no significant decrease (P>0.05), whereas polyphenol and flavonoid contents increased by 16.05% and 14.97%, respectively. The DPPH radical scavenging rate, hydroxyl radical scavenging rate, and ABTS⁺ radical scavenging rate reached 96.33%, 84.83%, and 98.37%, respectively. The antioxidant capacity of SL-Lpc was significantly higher than that of other samples (P<0.05). Correlation analysis demonstrated that polyphenolic compounds (including flavonoids) exhibited a significant positive correlation with in vitro antioxidant activity. Metabolomics analysis identified 16 phenolic acid metabolites (10 upregulated, 6 downregulated) and 12 flavonoid metabolites (9 upregulated, 3 downregulated) with differential abundance during fermentation. The up-regulation of multiple phenolic acids and the production of glycosidic flavonoids were the main reasons for the increased antioxidant activity after fermentation. This study will provide a reference for the development of wolfberry probiotic yoghurt.