As the three-dimensional (3D) molecular structure of kerogen plays important roles in further understanding of shale gas storage and transport, accurate characterization methods for 3D kerogen structures are attracting increasing attention. Spatial alignment is important information for 3D kerogen modeling, but was usually ignored in previous studies. In this work, seven kerogen samples with different maturities were isolated from organic-rich shale using a chemical method and highresolution transmission electron microscopy (HRTEM) was employed to quantitatively characterize the spatial alignment of these seven kerogen samples. Raman spectroscopy was used to investigate the overall structural disorder of the kerogen molecules and Fourier transform infrared (FT-IR) was conducted to study the chemical structure of these kerogen samples. The results show that immature, mature, and overmature kerogen samples all show an obvious alignment on the scale of 20 nm × 20 nm. In the immature kerogen sample Yl-1 with equivalent vitrinite reflectance (VR eqv ) = 0.4%, 60% of total aromatic fringes align in the major direction (with a 60°range), while 87% of the total aromatic fringes align in the major direction for the overmature kerogen sample Lmx-3 (VR eqv = 3.1%). However, unlike local alignment in the scale of 20 nm × 20 nm, the aromatic fringes in different regions may have different directions in larger scale. Meanwhile, based on FT-IR data, aliphatic carbons and oxygen containing functional groups contribute to a large proportion in immature, mature, and overmature kerogen samples. Thus, immature, mature and overmature kerogen samples all show overall disorder according to Raman data. In addition, the size of aromatic rings is also quantitatively characterized based on HRTEM images. In immature kerogen samples, the proportion of aromatic rings smaller than 3 × 3 is larger than 70%. In mature and overmature kerogen samples, 3 × 3 sized aromatic rings always occupy the largest proportion. This study provides the quantitative information on spatial alignment and the size of aromatic rings for kerogen samples, which contribute to an improved understanding of the 3D structure of kerogen.