The objective of this research was to compare the fermentability of three resistant starches (RS2, RS3, and RS5). Structural analyses showed that there were small changes in the long- and short-range ordered structure of three RSs after fermentation by human gut microbiota. The fermentation of RSs by gut microbiota produced large amounts of short-chain fatty acids, with RS5 producing more butyric acid and RS3 producing more lactic acid. RS3 and RS5 decreased the pH of the fermentation culture to a greater extent compared with RS2. Moreover, RS5 increased significantly the relative abundance of , , , , and . The results suggested that the form of RS was the main factor affecting the physiological function of RS and that RS5, as a recently recognized form of resistant starch, could be a better functional ingredient to improve health compared with RS2 and RS3.