In the present study, we prepared A- and B-type polymorph-resistant starch spherulites (RSSs) with a wide range of crystallinity, and elucidated the relation between crystalline structure and faecal microbial fermentation outcomes. A- and B-type polymorphic RSSs displayed similar fermentation rate throughout entire process with final gas production of 11.8–13.2 mL, suggesting that the crystalline pattern and crystallinity cannot effectively control the fermentation rate of starches. The acetate and butyrate concentration of A-type RSS decreased with the increase of crystallinity respectively, and highly crystalline B-type RSS reduced the production of acetate (8.4 mM) and propionate (2.1 mM). RSSs with different crystalline types showed similar microbial community structure but distinct key bacteria species. A-type RSSs greatly promoted the abundance of butyrogenic bacteria (i.e., Roseburia faecis and Lachnospiraceae), whereas B-type RSSs tended to proliferate Prevotella copri associated with propionate production. Our findings shed new light on design and manufacture of starch-based functional ingredients with enhanced gut health.