Xinjiang Ziziphus jujuba ‘Huizao’ wine, a characteristic fruit wine in China, is facing industrial bottlenecks such as flavor homogenization and lack of specialized fermentation yeasts, which limits its high-quality development. To solve these problems, four laboratory-preserved indigenous yeast strains (NZ5, NZ6, BH4, BH2) were compared with four commercial strains (FR, RW, RA, SY) in terms of fermentation dynamics, volatile flavor compound synthesis (HS-SPME-GC-MS/GC-FID), and sensory quality to screen the optimal yeast for Ziziphus jujuba ‘Huizao’ wine fermentation. Molecular identification revealed that NZ5 and NZ6 belong to Saccharomyces cerevisiae, while BH4 and BH2 are closely related to Pichia kudriavzevii, respectively, indicating their non-Saccharomyces characteristics with distinct metabolic potentials. The results showed that indigenous strains exhibited significantly superior performance to commercial strains: (1) Saccharomyces strains NZ5 and NZ6 had higher fermentation efficiency, with 12.5–25% shorter fermentation cycles and 14% higher cumulative CO₂ release than commercial strains; (2) Non-Saccharomyces strain BH4 synthesized the most diverse volatile flavors (99 compounds), with ethyl acetate content reaching 314.92 mg/L, which was 13-fold higher than that of commercial yeast FR (24.09 mg/L). Meanwhile, its phenethyl alcohol content reached 3.12 mg/L, 7.2 times that of commercial yeast RW; (3) Sensory evaluation showed that BH4-fermented wine had the highest score (88.59), significantly higher than commercial strains (63.57–67.67). In conclusion, BH4 is the optimal strain for improving the flavor quality of Xinjiang Ziziphus jujuba ‘Huizao’ wine, and NZ5/NZ6 are suitable for efficient industrial fermentation. This study provides valuable microbial resources and technical guidance for the quality improvement and industrial development of Xinjiang characteristic fruit wine.