Microorganisms produce hundreds of aroma-active compounds during fermentation process which affect the flavor of the final wine product. The current study explored the enological characteristics of non-Saccharomyces yeast strains and their influence on aroma compound complexity during fermentation process. Forty-two yeast strains were isolated from fruits by the DNA sequencing identification. Hanseniaspora uvarum Pi235, Pichia kluyveri Pe114, Saccharomyces cerevisiae Gr112 and Hanseniaspora guilliermondii Ki135 were selected for the following experiments due to the safety considerations and aroma diversity. Biochemical characteristics results showed that H. uvarum Pi235, P. kluyveri Pe114 and S. cerevisiae Gr112 exhibited different consumption preference in maltose, xylose and glycerol assimilation compared with their standard strains. Enological characteristics results showed that S. cerevisiae Gr112 exhibited best thermal tolerance, ethanol tolerance and β-glucosidase activity. Results of volatile aroma compounds analysis showed that non-Saccharomyces yeast strains were good at producing esters, such as ethyl acetate and 2-phenethyl acetate which were 11.8–25.4 and 4.1–15.2 folds higher than that from S. cerevisiae Gr112. Non-Saccharomyces yeast strains would provide more divers flavors in wines. The results will increase the applicability of non-Saccharomyces yeasts in the winemaking industry.