The authors present the first nanoscale imaging of X-ray diffraction in atomically thin superconducting BiSrCaCuO single crystals, employing the scanning X-ray nanobeam 100 nanometers wide. By simultaneously mapping the lattice and superlattice peaks over the crystal, they find that while the lattice peak position remains constant over the scan area, the superlattices peaks vary in position, reflecting mesoscale inhomogeneities. Remarkably, while the two types of superlattice peaks are correlated in k-space position in the bulk, they become anti-correlated when the crystals become two-unit cells thick. Reducing dimensionality towards atomic limit changes the lattice strain locally allowing raising of the new mesoscopic patterns, which controls charge distribution and material electronic properties.