Staple foods with starch and protein components are usually consumed after thermal processing. To date, how including protein hydrolysates (with varied hydrolysis degrees) tailors the structure and digestion features of starch-based matrix with thermal processing has not yet been sufficiently understood. Here, corn starch (CS), soy protein isolate (SPI), and soy protein isolate hydrolysates (SPIH) with different hydrolysis time (5–60 min) were used to prepare starch-based binary matrices. With the addition of SPI or SPIH during thermal processing, the resultant binary systems exhibited higher thermal stability (breakdown visibility was increased by 1.9–10.8 times), denser networks, and fewer short-range orders (R995/1022 was decreased by up to 15.3 %). These structural changes allowed an inhibited starch digestion within the binary system, especially with increased SPI or SPIH content. Compared with CS, the content of resistant starch (RS) for CS-SPI binary complex (10:3 w/w) increased from 9.89 % to 16.69 %. Compared to SPI, SPIH inclusion displayed a stronger inhibitory effect on starch digestion since the reduced molecule size of SPIH probably enhanced its interplays with starch or amylase. For instance, the 10:3 w/w starch-SPIH 60 binary matrix possessed the highest RS content (19.07 %).