This study compares continuous peptide-based enteral nutrition (PBF) with sequential standard polymer nutrition (SPF) in critically ill patients with acute gastrointestinal injury (AGI). This is a single-center, parallel-group randomized controlled trial in three clinical units of the Department of Intensive Care Medicine at the First Hospital of Jilin University, China. It will include 496 adult patients with AGI grades I–II who meet eligibility criteria in the final analysis, with 1:1 allocation and intention-to-treat analysis. In the PBF group, patients will receive continuous PBF fusion initiated within 7 days of admission to the ICU. In the SPF group, patients start PBF in the first 3 days and switch to SPF if AGI is grade 0–I on ICU day 4. The primary outcome measure is average daily energy intake on day 7 (kcal/kg/day). The study is registered under the identifier ChiCTR2200056858.