Microwave assisted drying methods, namely, microwave freeze drying (MFD) and microwave vacuum drying (MVD) were applied to dehydrate Chinese yam, with hot air drying (HA), freeze drying (FD) as contrast. The effects of drying methods on physico-chemical, functional, pasting, thermal and rheological properties as well as microstructure were evaluated. Resulted showed that the physico-chemical properties (e.g. content of polysaccharide, protein, total starch and apparent amylose content as well as bulk density, color) of yam flours were significantly affected by drying method. Functionally, the highest water binding capacity but lowest solubility was achieved by FD samples. The differences in thermal properties were presumed to be affected by protein retention to some extent. MFD flours presented the highest peak viscosity and final viscosity, while lower trend of retrogradation than that of FD flours. Rheological measurement demonstrated that all tested yam doughs exhibited solid-like behavior but variant intensity. Yam doughs produced by microwave assisted drying methods showed more solid-like property in cold paste (25 and 40 °C) as compared to that of FD as well as HA. Furthermore, the surface damage of yam starch granules was found in microwave assisted drying methods. These observations provided a deep understanding of the characteristics of Chinese yam flour affected by different drying methods, which would be conducive to their applications in food industry. •Best hydration was found in microwave freeze dried flour.•Microwave freeze dried flour can be used as thickener in food industry.•The highest long- and short-range order of starch was found in hot air dried flour.•Surface damage of starch granules was found in microwave assisted drying methods.