Gold nanoparticles (AuNPs) pose a great challenge in the development of nanotracers that can self‐adaptively alter their properties in response to certain cellular environments for long‐term stem cell tracking. Herein, pH‐sensitive Au nanotracers (CPP‐PSD@Au) are fabricated by sequential coupling of AuNPs with sulfonamide‐based polymer (PSD) and cell‐penetrating peptide (CPP), which can be efficiently internalized by mesenchymal stem cells (MSCs) and undergo pH‐induced self‐assembly in endosomes, facilitating long‐term computed tomography (CT) imaging tracking MSCs in a murine model of idiopathic pulmonary fibrosis (IPF). Using the CPP‐PSD@Au, the transplanted MSCs for the first time can be monitored with CT imaging for up to 35 days after transplantation into the lung of IPF mice, clearly elucidating the migration process of MSCs in vivo. Moreover, we preliminarily explored the mechanism of the CPP‐PSD@Au labeled MSCs in the alleviation of IPF, including recovery of alveolar integrity, decrease of collagen deposition, as well as down‐regulation of relevant cytokine level. This work facilitates our understanding of the behavior and effect of MSCs in the therapy of IPF, thereby providing an important insight into the stem cell‐based treatment of lung diseases.