Microorganism species and inoculation fermentation methods have great influence on physicochemical and flavor properties of rice wine. Thus, this work investigated microbial interactions and physicochemical and aroma changes of rice wine through different inoculation strategies of Wickerhamomyces anomalus (W. anomalus) and Saccharomyces cerevisiae (S. cerevisiae). The results underlined that inoculation strategies and non‐Saccharomyces yeasts all affected the volatile acidity, total acidity, and alcohol content of rice wine. The sequential cofermentation consumed relatively more sugar and resulted in the higher ethanol content, causing reduced thiols and increased alcohols, esters, phenylethyls, and terpenes, which was more conducive to improve rice wine flavor than simultaneous cofermentation. Moreover, simultaneous cofermentation increased fatty aroma of rice wine, while sequential cofermentation increased mellow and cereal‐like flavor. These results confirmed that sequential cofermentation of S. cerevisiae and W. anomalus was a choice for the future production of rice wine with good flavor and quality.