To understand the impact of different types of polyphenol-starch complexes on digestibility and gut microbiota, caffeic acid (CA) and corn starch (CS) complexes were prepared by coheating and high-pressure homogenization. The resistant starch content in CS coheated with CA (HCS-CA) and HCS-CA after high-pressure homogenization (HCS-CA-HPH) was 47.75 and 56.65%, respectively. Fourier transform infrared spectroscopy and X-ray diffraction analysis revealed hydrogen bonding in coheated samples and enhanced V-complex formation with high-pressure homogenization. The in vitro-digested complexes were of the B + V type, with higher relative crystallinity and short-range ordering of HCS-CA-HPH. Fermentation of the digested complex with human feces increased the yield of acetate, butyrate, and total short-chain fatty acids (SCFAs), which was more pronounced for HCS-CA-HPH. HCS-CA increased torques-Ruminococcaceae abundance, while HCS-CA-HPH boosted Prevotella, Roseburia, Lachnospiraceae, and Lachnospiraceae-NK4A136. Overall, CA and CS complexes enhanced beneficial bacteria and increased SCFA production.