Functional fermented fruit drinks are known worldwide for their health-promoting potential. Black wolfberry (BW) has high nutritional value, and its relative product development can be enriched through fermentation technology, so that its market might be broadened. Total acid, sugars, proteins, enzymes, anthocyanins, flavonoids, polyphenols, organic acids and DPPH free radical scavenging ability (DPPH) were tracked and determined by colorimetric method and HPLC during spontaneous fermentation of BW vinegar. The antioxidant capacity in vitro of BW vinegar was evaluated based on the dynamics of antioxidant contents and DPPH. The results showed that total acid continuously increased during fermentation, yet total sugar and reducing sugar shared a similar decreasing trend. The composition of samples differed in terms of total anthocyanins, total flavonoid, total polyphenol, total protein, superoxide dismutase (SOD), amylase, organic acids and DPPH through spontaneous fermentation. Functional compounds including total polyphenol, total flavonoid and three organic acids (γ-aminobutyric acid, lactic acid and gallic acid) played the main roles in antioxidation. Unexpectedly, SOD and ascorbic acid as antioxidants did not correlate with DPPH, but they were rich in the final products at 754.35 U/mL and 3.39 mg/mL, respectively. Generally, the quality of BW vinegar has been improved based on analyzing dynamics on functional compounds, organic acids and antioxidant capacity, which proves that BW vinegar obtained by spontaneous fermentation should be a potential source of fermented food with antioxidant effects for consumers.