Fluorescence imaging has emerged as a highly sensitive and real-time responsive modality for biomedical imaging. Within the near-infrared (NIR) tissue optical window, light absorption and light scattering of tissue are much lower, contributing to high signal-to-noise ratio, deep penetration and highly sensitive bioimaging. Quantum dots (QDs) have garnered significant attention as ideal fluoroprobes for imaging in organisms, owing to their unique and controllable optoelectronic properties arising from the quantum confinement effect. To address biotoxicity concerns, low biotoxicity heavy-metal-free QDs, including InP, CuInS2 and Ag-based QDs, are favored over their heavy metal containing (Cd, Hg, and Pb) counterparts. However, obtaining heavy-metalfree QDs emitting in the NIR window necessitates selective synthesis methods and QDs structure tuning, which remain challenging in achieving high quantum yield, redshift of the emission band and low permeability toxicity. Moreover, the successful construction of NIR QDs probes for diverse fluorescence imaging scenarios mandates a multi-strategy approach encompassing targeting, camouflage and timing considerations through appropriate surface modifications. This review focuses on heavy-metal-free NIR QDs for fluorescence imaging, considering performance modulation, optical properties of the materials and design strategies for bioimaging. Furthermore, it summarizes the persisting challenges and provides an outlook on the clinical application prospects of such materials.