The intricate topology of marginally twisted bilayers (twBL) plays a crucial role in twistronic investigation, determining their unique physical properties intertwined with accompanied moiré electronic properties. Despite the significance of this relationship, direct experimental elucidation of the corresponding atomic detail within individual sublayers is still lacking, limiting comprehensive exploration of the hidden twistronic electronic through twisted-moiré engineering. In this study, we first apply in-situ scanning tunneling microscopy/spectroscopy and non-contact atomic force microscopy to dissect the atomic structure of each sublayer in twBL transition metal dichalcogenides (twBL-TMDs) on the HOPG substrate. While electronic results show the expected rhombic-stacked moiré pattern, atomic structure measurements reveal an unexpected metastable topology, with the moiré-induced lattice displacement primarily affecting one sublayer—a departure from previous assumptions of equal displacement for each layer. The finding opens up innovative approaches for engineering moiré-induced topology, potentially enabling applications in functional twistronic devices.