Twisted bilayer systems host a wealth of emergent phenomena, such as flat-band superconductivity, ferromagnetism, and ferroelectricity, arising from moiré superlattices and unconventional interlayer coupling. Despite their central role, direct and quantitative access to the three-dimensional atomic arrangement in these systems has remained elusive due to their nanoscale dimensions. Here, we introduce an automated dark-field electron tomography technique that enables quantitative three-dimensional structural analysis of atomically thin materials with sub-Å precision. By applying this method to twisted bilayer WSe₂, we precisely visualize the twist-angle-dependent structural relaxation appearing as the AB/BA stacking domains separated by 10-20 nm domain walls.In the marginally twisted region (θ ≤ 0.1^∘), we uncover a significant expansion of the interlayer spacing compared to the bulk configuration, exceeding 0.1 Å, along with a remarkable temperature-driven interlayer decoupling. Ultrafast measurements further reveal optically induced interlayer separation of ~0.2 Å on the picosecond timescale, attributed to transient exciton formation. These findings not only establish a powerful approach for visualizing hidden out-of-plane structures in atomically thin micro-flake materials, but also uncover the intrinsic fragility and dynamical tunability of interlayer coupling in moiré-engineered 2-dimensional materials.