Starch‐containing foods with a high glycemic index and deficiency protein cannot meet the consumers’ proactive demand. Thus, the objective of this work is to test the effect of the presence of grass carp protein hydrolysates (GCPHs) on the digestive and structural properties of pristine rice starch (PRS) during the treatment of high pressure homogenization in combination with spray‐drying (HPH‐SP), and its possible mechanisms. The results show that, when the mass ratio of PRS: GCPHs increases from 100:0 to 100:15 during HPH‐SP treatment, the presence of GCPHs significantly increases the contents of slowly digestible starch (SDS) from 7.8 to 23.0%, and resistant starch (RS) from 10.7 to 25.3% in PRS‐GCPHs complexes after gelatinization, respectively. Structures based on SEM, XRD, ATR‐FTIR, and SAXS show that, compared to HPH‐SP treatment alone, HPH‐SP treatment in the presence of GCPHs can remarkably destroy crystallinity, shorten branch chain content, lower the IR ratio of 1045/1022 cm−1, bragg spacing and lamellar peak intensity of PRS, and strengthen rigidity of PRS‐GCPHs complexes granules, which can play a significant role in increasing the contents of SDS and RS. Moreover, gelatinized PRS‐GCPHs rapidly assembles and aggregates to form more space hindrance and inhibit amylase close to leaching amylose, chained, or even branched amylopectin, which can be also attributed to the increased contents of SDS and RS authenticated by the observations of RVA, AFM, and representative images. These findings suggest that the presence of GCPHs during HPH‐SP treatment can be potently employed for preparing in vitro low digestible starch.