Goaty flavor and poor consistency may have certain impact on consumer acceptance of goat milk yogurt. The special flavor and poor consistency may be mainly attributed to the presence of short-medium chain free fatty acid (SM-FFA) especially C6-C10 fatty acids and low casein content in goat milk. This study aimed to investigate the effects of polymerized whey protein (PWP) on goaty flavor as well as texture of goat milk yogurt compared with β-cyclodextrin (β-CD). Samples were evaluated on sensory properties, SM-FFA contents, texture, and viscosity. Compared with control, the contents of fatty acids (C6, C8, C10) of the yogurt samples significantly decreased approximately by 22%, 71%, 54% in goat milk yogurt with 0.5% β-CD while they decreased approximately by 45%, 58%, 71%, respectively, with 0.7% PWP. There was a synergistic effect of 0.3% β-CD and 0.6% PWP by decreasing the contents of SM-FFA (C6, C8, C10) sharply by 89%, 90%, 79%. Under the same percentage of addition in the yogurts with β-CD showed a higher (P < 0.05) viscosity than those with PWP. However, addition of PWP increased the texture parameters of goat milk yogurt (P < 0.05). Combination of PWP and β-CD presented a more desirable texture and consistency in goat milk yogurt. Results indicated that polymerized whey protein can be used to reduce the goaty flavor and improve the texture of goat milk yogurt.