Quantum devices exploiting twistronics by stacking two-dimensional materials could enable breakthroughs in computing and sensing beyond the limits of current transistors. Scaling up these devices poses grand challenges for in situ metrology, because existing tools lack the accuracy for characterizing sub-atomic structures. Here we demonstrate a laser-based interferometric method, termed Phase Amplification microscopy ({\Phi}-Amp), which can push the measurement accuracy limit to the femtometer-level and beyond in ambient conditions. We show {\Phi}-Amp amplifies weak phase signals from graphene by over 100 times through devising a phase cavity based on a novel phase-gain theory, enabling real-time, wide-field mapping of atomic layers with picometer-level accuracy. We quantified interlayer spacing differences between AB-stacked and 30-degree-twisted bilayer graphene to be ~ 0.71 {\AA}, a subtle distortion driven by quantum interactions that was previously inaccessible to in situ metrology. We envision {\Phi}-Amp as a transformative tool for both expediting wafer-scale atomic fabrication and advancing research in quantum materials by probing subatomic phenomena.