Nanomaterials with unique physical and biological properties have attracted increased attention for bio-microimaging applications. Among them, lowdimensional nanomaterials have quantum confinement effect in zero, one, or two dimensions, which have high specific surface area for cargo (such as dye) loading, anisotropic optical properties for polarization, and enhanced infrared absorption for efficient photoluminescence. In this review, recent efforts on bio-microimaging of low-dimensional nanomaterials, including confocal imaging, multiphoton imaging, Raman imaging, and super-resolution imaging, will be highlighted. Bio-microimaging principle, respective advantages and bottlenecks, and applications of low-dimensional materials in various imaging technologies will be discussed. Furthermore, the review will shed light on the common synthetic methods of low-dimensional nanomaterials. Finally, the classification and comparison of various nanomaterials, including carbon, black phosphorus, gold, metal composites, and 2D graphene analogues will also be elaborated.