Rutin is a flavonoid polyphenol with excellent biological activity, but due to its instability and poor water solubility, the utilization rate is reduced in vivo. Preparation of rutin microcapsules from soybean protein isolate (SPI) and chitosan hydrochloride (CHC) by composite coacervation can improve this restriction. The optimal preparation conditions were as follows: the volume ratio of CHC/SPI 1:8, pH 6, and total concentration of CHC and SPI 2 %. The rutin encapsulation rate and loading capacity of the microcapsules were 90.34 % and 0.51 % under optimal conditions. The SPI-CHC-rutin (SCR) microcapsules had a gel mesh structure and good thermal stability, and the system was stable and homogeneous after 12 d storage. During in vitro digestion, the release rates of SCR microcapsules in simulated gastric and intestinal fluids were 16.97 % and 76.53 %, respectively, achieving a targeted release of rutin in intestinal fluids; and the digested products were found to exhibit superior antioxidant activity to that of free rutin digests, indicating a good protection of microencapsulation on the bioactivity of rutin. Overall, SCR microcapsules developed in this study effectively enhanced the bioavailability of rutin. The present work provides a promising delivery system for natural compounds with low bioavailability and stability.