The research of structure of coal and kerogen is enhanced by innovation of technology and methodology. From early chemical depolymerization to physical method and then to computer aided molecular modeling, many structural models of coal and kerogen are built up. However, no structural model is widely accepted  as the heterogeneity and structural complexity of coal and kerogen enhance the difficulty to illustrate their physical and chemical structure. Nanotechnology greatly promotes the research and knowledge of structure of coal and kerogen. Atomic Force Microscopy (AFM) is a representative example. As result of real-time, real-space, in-situ imaging and ability to partly observe surface structure of single molecular layer, AFM can directly observe the morphology and position of surface defect, surface reconstruction and surface adsorbate and even dynamic process such as surface diffusion. AFM surpasses conventional 2D plane imaging and provides 3D dynamic images  and quantitative information. Realizing atomic level resolution and revealing the morphology, size, structure and spatial arrangement of molecular aggregates and nanopores of coal and kerogen, nanotechnology shows great potential in structural research of coal and kerogen. Nanotechnology provides new approaches for basic research of coal and kerogen and supports exploration and exploitation of unconventional oil and gas and research of coal secondary transformation with scientific evidence.