Small-molecule near-IR (NIR) optical imaging has experienced tremendous advancements over the past two decades, playing important roles in both theory and application in the biomedical field. NIR optical imaging affords improved contrast and depth of tissue penetration by reducing photon scattering, lowering tissue absorption, and minimizing autofluorescence in the NIR window. Moreover, molecular engineering endows small-molecule probes with powerful tunability, providing a valuable means for real-time noninvasive visualization of various biological processes and analytes in vivo with high sensitivity and resolution. In this review, we focus on the most recent advances in the development of small-molecule NIR probes and their applications in bioimaging. We also highlight the challenges and opportunities in this rapidly developing field.