The application of NIR‐II emitters for gastrointestinal (GI) tract imaging remains challenging due to fluorescence quenching in the digestive microenvironment. Herein, we report that red‐shifting of the fluorescence emission of Au nanoclusters (AuNCs) into NIR‐II region with improved quantum yields (QY) could be achieved by engineering a protein corona structure consisting of a ribonuclease‐A (RNase‐A) on the particle surfaces. RNase‐A‐encapsulated AuNCs (RNase‐A@AuNCs) displayed emissions at 1050 nm with a 1.9 % QY. Compared to rare earth and silver‐based NIR‐II emitters, RNase‐A@AuNCs had excellent biocompatibility, showing >50‐fold higher sensitivity in GI tract, and migrated homogenously during gastrointestinal peristalsis to allow visualization of the detailed structures of the GI tract. RNase‐A@AuNCs could successfully examine intestinal tumor mice from healthy mice, indicating a potential utility for early diagnosis of intestinal tumors.