Knowledge of the atomic structure of layer-stacked two-dimensional conjugated metal-organic frameworks (2D c-MOFs) is an essential prerequisite for establishing their structure-property correlation. For this, atomic resolution imaging is often the method of choice. In this paper, we gain a better understanding of the main properties contributing to the electron beam resilience and the achievable resolution in the high-resolution TEM images of 2D c-MOFs, which include chemical composition, density, and conductivity of the c-MOF structures. As a result, sub-angstrom resolution of 0.95 Å has been achieved for the most stable 2D c-MOF of the considered structures, Cu₃(BHT) (BHT = benzenehexathiol), at an accelerating voltage of 80 kV in a spherical and chromatic aberration-corrected TEM. Complex damage mechanisms induced in Cu₃(BHT) by the elastic interactions with the e-beam have been explained using detailed ab initio molecular dynamics calculations. Experimental and calculated knock-on damage thresholds are in good agreement.