In recent years, magnetic resonance imaging (MRI) has become more widely used in neonatal hypoxic-ischemic encephalopathy (HIE), involving, for example, evaluation of cerebral edema, white matter fiber bundle tracking, cerebral perfusion status, and assessment of brain metabolites. MRI has many imaging modalities. However, its application for assessing changes in the internal environment at the tissue and cellular level after hypoxia-ischemia remains a challenge and is currently the focus of intense research. Based on the exchange between amide protons of proteins and polypeptides and free water protons, amide proton transfer (APT) imaging can display changes in pH and protein concentrations in vivo. This paper is a review of the principles of APT imaging, with a focus on the potential application of APT imaging for neonatal HIE.