Lacticaseibacillus rhamnosus (L. rhamnosus) is a probiotic strain that has exhibited probiotic properties in the prevention and treatment of intestinal flora imbalance. In order to investigate the morphological differences and molecular mechanisms underlying the effects of simulated gastrointestinal digested soybean protein isolate (dpro22dpro: digested soybean protein isolate, dpep: digested soybean peptide, M: Man Rogosa Sharpe broth, DAPs: Differentially abundant proteins. dpep/M: dpep sample relative to the M sample, dpro/M: dpro sample relative to the M sample, dpep/dpro: dpep sample relative to the dpro sample.) and digested soybean peptide (dpep) treatment on L. rhamnosus, microscopic observation and iTRAQ-based proteomics and bioinformatics analysis were performed. 1462 proteins were identified, and differentially abundant proteins (DAPs) were screened accurately, including 66 DAPs in the dpep group compared with the Man Rogosa Sharpe broth (M) group and 66 DAPs in the dpep/dpro group. Bioinformatic analysis revealed that DAPs in dpep/M and dpep/dpro mainly differed in cellular carbohydrate and nitrogen compound catabolic processes and transport. Some of the DAPs overlapped in the three comparison groups might be pivotal proteins involved in growth and morphologic changes of the dpep and dpro treatments.