To clarify the overall quality differences among cows', goats', and camels' milk powder fermented yoghurts, this study evaluated the physical and chemical properties of cow milk yoghurt, goat milk yoghurt, and camel milk yoghurt, and then compared the main components and amino acid composition, volatile aroma components, texture profile analysis, and rheological characteristics. Results showed that cow milk yoghurt had the best structural stability; goat milk yoghurt had the most abundant fat content (4.15 ± 0.40 g 100 g−1) and volatile aroma components, but the relative content of acids was the highest, which is not favourable to the flavour of goat milk yoghurt. Camel milk yoghurt had the highest antioxidant activity, cysteine (0.15 ± 0.05 mg g−1) and protein content (3.69 ± 0.14 g 100 g−1), and lowest lactose content (4.37 ± 0.01 g 100 g−1). The research showed differences in the quality of yoghurts from three different animal sources and will help increase our knowledge of specialty dairy products.