The development of rapidly distributed and retained probes within the kidneys is important for accurately diagnosing kidney diseases. Although molecular imaging shows the potential for non‐intrusively interrogating kidney disease‐related biomarkers, the limited kidney contrast of many fluorophores, owing to their relatively low distribution in the kidney, hinders their effectiveness for kidney disease detection. Herein, for the first time, an amino‐functionalization strategy is proposed to construct a library of kidney‐targeting fluorophores NHcy with tunable emissions from NIR‐I to NIR‐II. Among these, NHcy‐8 is the first small‐molecule NIR‐II dye without a renal clearance moiety, designed specifically for kidney‐targeting imaging. Building on this class of NIR‐II fluorophore, the first NIR‐II small‐molecule kidney‐targeting pH probe NIR‐II‐pH is developed, which exhibits a desirable kidney distribution after intravenous injection and is fluorescent only after activation by acidosis. NIR‐II in vivo fluorescence/photoacoustic imaging of kidney disease models induced by cisplatin and renal I/R injury using NIR‐II‐pH reveals increasingly severe metabolic acidosis as the disease progressed, enabling sensitive detection of the onset of acidosis 36 h (cisplatin group) earlier than clinical methods. Thus, this study introduces a practical NIR‐II kidney‐targeting probe and provides a useful molecular blueprint for guiding kidney‐targeting NIR‐II fluorophores as diagnostic aids for kidney diseases.