Spray-dried whey protein powders were produced from whey obtained as a by-product in the production of milk cake and milk fan as ethnic dairy products in Yunnan, and their main components and processing characteristics were analyzed. The results showed that the main components of whey protein powder obtained from the by-product of milk cake were protein 39.0%, fat 6.0%, moisture 4.1%, total ash 7.7%, acidity 23.2 °T, and pH 5.61, and the processing characteristics were 99.52% solubility, less than 3.2% precipitation at different temperatures, and emulsifying activity index (EAI) and emulsion stability index (ESI) both greater than 42.7% at different pH values. The main components in whey protein powder obtained from the by-product of milk fan were protein 72.0%, fat 19.8%, moisture 4.6%, total ash 8.1%, acidity 58.3 °T, and pH 5.20, and its processing characteristics were 98.70% solubility, less than 3.5% precipitation at different temperatures, and EAI and ESI both higher than 50% at different pH values. The sensory scores of yogurts with the two whey protein powders were 70.7 and 72.7 out of 100 points, respectively, indicating that both can be used as an ingredient in yogurt.