The object of this study was to compare the effects of three indigenous non-Saccharomyces cerevisiae strains (Hanseniaspora uvarum, Metschnikowia sinensis and Rhodotorula mucilaginosa) and their paired (co-inoculated) fermentation on the microbial communities and volatile profiles during the fermentation of Marselan wine. Results showed that both monoculture and mixed fermentation with non-Saccharomyces strain can complete alcohol fermentation wherein the alcohol content of indigenous yeast treatments were significantly higher than that of control NSD. A total of 44 aroma compounds were identified in all samples, among which the H + R mixed inoculation showed the highest aroma content (28581±1576.61 μg/L). In particular, the contents of ethyl butyrate (V5), ethyl octanoate (V9), and ethyl decanoate (V11) were significantly high, which could enhance the fresh fruit aroma in Marselan wine. Microbial diversity analysis showed that the diversity of fungi between groups was greater than that of bacteria, and H + R (Hanseniaspora and Rhodotorula) had higher microbial abundance (bacteria 79, fungi 78) than the other groups. Spearman correlation analysis revealed that Fructobacillus, Acinetobacter, and other indigenous microorganisms were positively correlated with volatile substances. In summary, the mixed fermentation of Hanseniaspora and Rhodotorula can be considered an effective strategy for improving the aroma quality of Marselan wine. This study provides new insight and useful references for the role and application of native non-Saccharomyces yeast in wine making.