The structures of covalent organic frameworks (COFs) are typically determined through modeling based on powder X-ray diffraction. However, the intrinsically limited crystallinity of COFs often results in structural determinations of low fidelity. Here, we present real-space imaging of an extensively studied two-dimensional imine-based COF. Contrary to the conventional understanding that this COF features uniform hexagonal pores, our observations reveal the presence of two distinct sets of pores with differences in shape and size. Motivated by this finding, we conducted reciprocal-space characterizations, complemented by solid-state nuclear magnetic resonance spectroscopy and density functional theory calculations, to reevaluate this seemingly simple structure. The collective results allow for the establishment of a new structural model for this landmark COF and its derivatives, differing from the conventional model in both intra- and interlayer configurations. Furthermore, we identified various previously unrecognized defective structures through real-space imaging, which have significant implications for COF applications in separation and catalysis. Our study demonstrates the complexity and heterogeneity of COF structures, while also highlighting the imperative for structural reevaluation using advanced characterization techniques.