In this study, the effect and mechanism of pectin on the inhibition of in vitro starch digestion by a mixture of flavanols (rutin, quercetin, and kaempferol [R–Q–K]) were investigated, mainly from an enzymatic point of view. Results showed that the association of pectin and R–Q–K decreased the hydrolysis rate, rapidly digestible starch content, estimated glycemic index (eGI) values and hydrolysis index (HI) values, and increased the resistant starch content of different crystalline starches. Among them, cassava starch exhibited a significant decrease in terms of HI and eGI values (32.81% ± 0.65% and 10.57% ± 0.37%, respectively). Meanwhile, the lowest rate of decrease in terms of HI and eGI values was found for breadfruit starch (22.97% ± 0.39% and 7.23% ± 0.62%, respectively). The inhibitory effect of R–Q–K on α-glucosidase was attenuated by low concentrations of pectin, which was correlated to the non-covalent binding among pectin, α-glucosidase, quercetin, and kaempferol. The hydrogen bonding between pectin–R–Q–K and starch may be responsible for the ability of low concentrations of pectin and R–Q–K to synergistically delay starch digestion. Higher concentrations of pectin were noted to have the opposite trend, which was attributed to forming the binary complex of pectin–α-glucosidase. The inhibitory affinity and quenching affinity of R–Q–K for α-glucosidase were enhanced by low concentrations of pectin and attenuated by high concentrations of pectin. This study aims to provide theoretical support for the development of pectin and flavonoids in starch-based healthy foods.