Soybean is one of the essential ingredients when formulating a tube feeding formula. In this study, we initially focused on determining which enzyme is suitable for hydrolyzing soy and comparing the soy protein enzymatic hydrolysis of three different enzymes at the same enzyme content: Flavourzyme, Protamex, and Alcalase. The result showed that Flavourzyme attained the highest soluble protein recovery efficiency (SPRE). Secondly, the study determined the effect of thermal treatment conditions such as thermal treatment duration, and then it showed that when combining the thermal treatment and enzymatic hydrolysis, the yield reached (61.44 ± 0.22)%, which was much higher than only using enzymatic hydrolysis (52.57 ± 0.27)%. Next, optimizing the enzymatic hydrolysis (combining thermal treatment) using Flavourzyme and Alcalase, Flavourzyme achieved (62.47 ± 0.12)%, while Alcalase attained (41.32 ± 0.13)%. The soy hydrolyzate using Flavourzyme achieved an average molecular size of 3.19 kDa at the following optimizing conditions: enzyme concentration, 16.09 U·g⁻¹; pH, 7.02; temperature, 45.8 °C; and beans/water ratio, 1:3. In contrast, when using Alcalase, the soy hydrolyzate achieved an average molecular size of 1.52 kDa at the following optimizing conditions: enzyme concentration, 28.01 U·g⁻¹; pH, 7.2; temperature, 56.5 °C; beans/water ratio, 1:4.6. Soy protein hydrolyzate of suitable viscosity and particle size flow through the inhaler with branched-chain amino acids achieved a BCAA (Branched Amino Acid) ratio of 2:1:1 for Alcalase and 4:1:1 for Flavourzyme. Soybean hydrolyzate using both enzymes attained a high SPRE and was suitable for the digestive ability of patients recovering from surgery. Soy protein is divided into amino acids, di- and tri-amino acids, and peptides to create a soluble protein source that helps feed patients with a sonde tube easily. In addition, the molecular weight of peptides will reduce viscosity significantly when passing through a sonde tube, preventing tube congestion.