As Gd-based contrast agents suffer from the risk of causing nephrogenic systemic fibrosis, less toxic contrast agents are urgently needed in contrast-enhanced magnetic resonance imaging (CE-MRI) of kidney injury. Herein, we develop a non-invasive diagnosis method for acute kidney injury using CE-MRI based on manganese-doped carbon dots (Mn-CDs). The synthesized Mn-CDs possess an ultrasmall size of 5 nm, good biocompatibility, and a high T1 relaxation rate (10.8 mM-1 s-1), which can produce effective positive enhancement in the kidneys and clearly show the fine structures of the kidneys including the cortex, outer medulla, and inner medulla. In an acute kidney injury model, Mn-CDs-based CE-MRI can not only accurately and intuitively reveal the site of kidney injury consistent with the pathological analysis, but also reflect the functional changes in the injured kidney. Collectively, our study provides a new strategy for the non-invasive diagnosis of acute kidney injury using CE-MRI based on Mn-CDs.