Directly imaging the configurations of small molecules at the ambient temperatures will greatly promote the study of their chemical and physical properties, including the host-guest interactions of organics in porous materials during the adsorption, catalysis and energy storage. However, due to the current challenges on the small-molecule imaging by the (scanning) transmission electron microscopy ((S)TEM), we still have a lack of the molecular-level understandings on the host-guest interactions and other molecular behaviors. Here, we achieved the STEM imaging of various small aromatics confined in the MFI-type zeolite frameworks by using the integrated differential phase contrast (iDPC) technique. Due to the strong confinement effect in MFI channels, the 1D solid-like aromatic columns showed the coherent configurations, which were clearly resolved by enhancing the host-guest interactions. Then, we also evaluated the strength of host-guest interactions directly by the image analysis and revealed the desorption behaviors of confined aromatics during the in-situ heating process. These results not only helped us to reveal the configurations and host-guest interactions of small aromatics during the adsorption/desorption in porous materials, but also expanded the applications of STEM to further study other molecular behaviors in the real space.