Utilizing Atomic Force Microscopy (AFM) to observe the surface structure of barkinite and vitrinite of "barkinite" liptobiolith in nanoscale, reveal the surface microstructures of barkinite and vitrinite, that is, the netlike structure of vitrinite macromolecular clusters and the fiberlike, granular, and netlike structure of barkinite macromolecular clusters. With the increasing of maturity, the structure of barkinite macromolecular clusters are fiberlikegranularirregular netlikenetlike in sequence, while the structure of vitrinite macromolecular clusters change from loose, irregular network to highly orient arranged, regular network. Quantitative analyze of the structure of macromolecular cluster and arrangement in maceral by using Atomic Force Microscopy cross section analyze tool provide a new approach to study the structure evolution of maceral molecule and hydrocarbon generation mechanism.