Abstract: Carbon, as an indispensable chemical element on Earth, has diverse covalent bonding ability, which enables construction of extensive pivotal carbon-based structures in multiple scientific fields. The extraordinary physicochemical properties presented by pioneering synthetic carbon allotropes, typically including fullerenes, carbon nanotubes, and graphene, have stimulated broad interest in fabrication of carbon-based nanostructures and nanomaterials. Accurate regulation of topology, size, and shape, as well as controllably embedding target spⁿ-hybridized carbons in molecular skeletons, is significant for tailoring their structures and consequent properties and requires atomic precision in their preparation. Scanning probe microscopy (SPM), combined with on-surface synthesis strategy, has demonstrated its capabilities in fabrication of various carbon-based nanostructures and nanomaterials with atomic precision, which has long been elusive for conventional solution-phase synthesis due to realistic obstacles in solubility, isolation, purification, etc. More intriguingly, atom manipulation via an SPM tip allows unique access to local production of highly reactive carbon-based nanostructures. In addition, SPM provides topographic information of carbon-based nanostructures as well as their characteristic electronic structures with unprecedented submolecular resolution in real space. In this review, we overview recent exciting progress in the delicate application of SPM in probing low-dimensional carbon-based nanostructures and nanomaterials, which will open an avenue for the exploration and development of elusive and undiscovered carbon-based nanomaterials.