Near-infrared (NIR) transparency windows have evoked considerable interest in biomedical thermal imaging owing to the superior tissue penetration and the high signal-to-noise ratio, allowing in vivo real-time temperature reading with nanometric spatial resolution. Here, we develop a multimode nonintrusive luminescent thermometer based on the Y3Al5O12 (YAG):Cr3+/Ln3+ (Ln = Ho, Er, Yb) phosphor, which covers three NIR biological transparency windows, enabling cross-checking readings with high sensitivity and a high penetration depth. Utilizing the energy transfer between lanthanide ions and transition-metal ions, the Cr3+/Ln3+-activated upconversion emissions provide ideal signals for ratiometric luminescent thermometry of the NIR-I mode. The phonon-assisted downshifting emissions of Er3+/Ho3+ are used to construct the NIR-III/II mode, and the NIR-III mode is based on the thermal coupling between stark levels of 4I13/2 (Er3+). Three independent modes show distinct thermometric performance in different NIR transparency windows and temperature ranges, and the combination of the three modes is conducive to obtain more accurate temperature readings in a broad temperature range, which paves the way toward versatile luminescent thermometers.