The green separation of soy protein enzymatic hydrolysates (SPEH) with different flavors can enhance the application of SPEH in the food industry. This study investigated the detailed process of separating and purifying SPEH by utilising the interaction between SPEH and adsorptive resins, and the mass transfer behaviour of SPEH in the adsorptive resin was explored by a mathematical model. Initially, soybean meal underwent hydrolysis by papain. Subsequently, the resulting SPEH was adsorbed onto the resin under various pH conditions and then desorbed. In general, SPEH exhibited a greater ability to bind with the resin under protonation treatment (pH 3.0) compared to deprotonation treatment (pH 9.0). The equilibrium adsorption capacity at pH 3.0 and 9.0 was 33.1 ± 1.7 mg g−1 and 24.1 ± 0.9 mg g−1, respectively. At the same time, SPEH exhibited greater surface diffusivity within the resin during adsorption at pH 3.0 (2.83 × 10−8 cm2 s−1) compared to pH 9.0 (2.41 × 10−8 cm2 s−1). Due to the robust binding affinity of SPEH with the resin in the acidic environment, a smaller quantity of SPEH was released from the resin during the subsequent desorption process. Furthermore, the bitter SPEH, characterised by an abundance of random coil and β-turn structures, demonstrated greater affinity for binding with the adsorptive resin compared to the salty and umami SPEH, which exhibited a higher proportion of β-sheet structure. After adsorption at pH levels ranging from 3.0 to 9.0 and subsequent desorption, the recovery of SPEH ranged from 30.4 % to 35.7 %, with purities between 57.5 % and 62.3 %. Overall, this study offers valuable insights into the targeted separation of various flavor components from SPEH, shedding light on the intricate dynamics of adsorption and desorption processes under different pH conditions.