Fluorescence bioimaging affords a vital tool for both researchers and surgeons to molecularly target a variety of biological tissues and processes. This review focuses on summarizing organic dyes emitting at a biological transparency window termed the near‐infrared‐II (NIR‐II) window, where minimal light interaction with the surrounding tissues allows photons to travel nearly unperturbed throughout the body. NIR‐II fluorescence imaging overcomes the penetration/contrast bottleneck of imaging in the visible region, making it a remarkable modality for early diagnosis of cancer and highly sensitive tumor surgery. Due to their convenient bioconjugation with peptides/antibodies, NIR‐II molecular dyes are desirable candidates for targeted cancer imaging, significantly overcoming the autofluorescence/scattering issues for deep tissue molecular imaging. To promote the clinical translation of NIR‐II bioimaging, advancements in the high‐performance small molecule–derived probes are critically important. Here, molecules with clinical potential for NIR‐II imaging are discussed, summarizing the synthesis and chemical structures of NIR‐II dyes, chemical and optical properties of NIR‐II dyes, bioconjugation and biological behavior of NIR‐II dyes, whole body imaging with NIR‐II dyes for cancer detection and surgery, as well as NIR‐II fluorescence microscopy imaging. A key perspective on the direction of NIR‐II molecular dyes for cancer imaging and surgery is also discussed. Among all existing near‐infrared (NIR)‐II fluorophores, the NIR‐II molecular dyes are the most remarkable in translating this imaging window into the clinical setting. Advanced NIR‐II dye‐derived bioconjugates will give doctors an unparalleled view into tissues for tumor detection at greater depths and contrast, allowing early detection during cancer screenings and solid tumor resection by delineation of the boundaries between healthy and cancerous tissues.