Dendrobium officinale (DO), a valuable Chinese herb exhibiting enormous health benefits, has gained recognition as a functional food. DO contains abundant bioactive compounds, such as polysaccharides, dendrobine, flavonoids, amino acids, and volatile compounds and has been used to enhance the flavor and bioactive compounds in yogurt. This study aimed to explore the effects of DO on the physicochemical characteristics and flavor properties of yogurt at different fermentation times. The volatile compound profiles, concentration, and odor activity value (OAV) of yogurt at different fermentation times were assessed. The addition of DO reduced the pH and increased the acidity, apparent viscosity, and water-holding capacity. Furthermore, DO addition had a significant effect on the volatile compounds in fermented milk, which also significantly changed during the fermentation process. 2-Heptanone was identified as the major contributor to yogurt flavor at different fermentation times. Hierarchical cluster analysis revealed two significantly different clusters for the samples based on the concentration of the main compounds in samples obtained at different fermentation time points. Cluster 1 comprised the samples obtained at 1, 3.5, and 3 h of fermentation, whereas the other cluster comprised the samples at 1.5, 2, 2.5, and 4 h of fermentation. Additionally, certain unique compounds emerged or diminished depending on the fermentation time. These findings offer valuable insights for future reference in the development and quality control processes of DO-supplemented yogurt.