(1) Background: Flavored craft beer is favored for its diverse and distinctive aroma compounds; however, traditional fermentation processes are often plagued by poor yeast flocculation, which leads to substantial beer losses and compromised production efficiency. Yeast immobilization technology has emerged as a promising strategy to improve fermentation performance, shorten the primary fermentation period, and mitigate beer loss. (2) Methods: In this study, a natural material–based carrier was developed for the immobilization of yeast, and its application in mango craft beer fermentation was systematically investigated. The optimal fermentation conditions were screened, and the physicochemical properties, nutritional composition, and volatile flavor profiles of the resulting mango craft beer were comprehensively evaluated. (3) Results: The results showed that the maximum mass gain of yeast after immobilization on the natural carrier reached 13.3%. Compared with free yeast, the immobilized yeast exhibited 1.58-fold higher average extract consumption rate and 1.39-fold higher alcohol production rate, while the primary fermentation period was shortened by approximately 33%. Under the optimized fermentation conditions, the mango craft beer achieved a sensory score of 81 points, with a β-carotene retention rate of 91.25%. Furthermore, the mango craft beer exhibited a more diverse profile of volatile flavor compounds and enhanced nutritional composition compared with the control. (4) Conclusions: Overall, the natural immobilization carrier developed in this study effectively enhanced yeast fermentation efficiency, shortened the primary fermentation cycle. These findings demonstrate its significant potential for cost reduction and efficiency enhancement in the production of flavored craft beer, providing a practical technical support for the industrial application of natural carrier-based yeast immobilization technology.