This study examined the effect of calcium hydroxide (Ca(OH)2, 0.6%, w/w) on structural, physicochemical and in vitro digestibility properties of the complexed system of Tartary buckwheat starch (TBS) and rutin (10%, w/w). The pre-gelatinization and co-gelatinization methods were also compared. SEM results showed that the presence of Ca(OH)2 promoted the connection and further strengthened the pore wall of the three-dimensional network structure of the gelatinized and retrograded TBS-rutin complex, indicating the complex possessed a more stable structure with the presence of Ca(OH)2, which were also confirmed by the results of textural analysis and TGA. Additionally, Ca(OH)2 reduced relative crystallinity (RC), degree of order (DO) and enthalpy, inhibiting their increase during storage, thereby retarding the regeneration of the TBS-rutin complex. A higher storage modulus (G') value was observed in the complexes when Ca(OH)2 was added. Results of in vitro digestion revealed that Ca(OH)2 retarded the hydrolysis of the complex, resulting in an increase in values in slow-digestible starch and resistant starch (RS). Compared with pre-gelatinization, the complex process prepared with the co-gelatinization method presented lower RC, DO, enthalpy, and higher RS. The present work indicates the potential beneficial effect of Ca(OH)2 during the preparation of starch-polyphenol complex and would be helpful to reveal the mechanism of Ca(OH)2 on improving the quality of rutin riched Tartary buckwheat products.