To investigate the changes of the main ingredients in black garlic (BG) during fermentation, the contents of moisture, total acids and reducing sugars were determined. Allicin, 5-Hydroxymethylfurfural (5-HMF), and total phenols were also determined as bioactive substances. DPPH scavenging capacity was determined to indicate the antioxidant activity of BG. The changes in hardness and color were detected as well. The results showed that the moisture content decreased from 66.13% to 25.8% during the fermentation. The content of total acids, total phenols, and reducing sugars increased from 0.03 g/g to 0.29 g/g, from 0.045 μg/g to 0.117 μg/g, and from 0.016 g/g to 0.406 g/g, respectively. The content of 5-HMF increased from 0 to 4.12 μg/mL continuously, while the content of allicin increased from 0.09 mmol/100 g to 0.30 mmol/100 g and then decayed to 0.00 mmol/100 g. The L*, a*, and b* values of BG were 23.65 ± 0.44, 0.64 ± 0.06, and 0.85 ± 0.05, respectively. There was a higher intensity of dark color in BG than that in fresh garlic. The hardness values decreased first and then increased in later fermentation from 465.47 g to 27,292.38 g. Principal component analysis (PCA) showed that the samples were divided into three clusters, including cluster1 (fresh garlic, S0), cluster2 (S1), and cluster3 (S3−S9). This research effectively clarified the various stage of the BG fermentation process, and it is expected to supply references for reducing production time in industrial BG fermentation.