Accurate investigations of quantum-level energies in molecular systems are shown to provide a testing ground to constrain the size of compactified extra dimensions. This is made possible by recent progress in precision metrology with ultrastable lasers on energy levels in neutral molecular hydrogen (H2, HD, and D2) and molecular hydrogen ions (H2+, HD+, and D2+). Comparisons between experiment and quantum electrodynamics calculations for these molecular systems can be interpreted in terms of probing large extra dimensions, under which conditions gravity will become much stronger. Molecules are a probe of spacetime geometry at typical distances where chemical bonds are effective (i.e., at length scales of an Å). Constraints on compactification radii for extra dimensions are derived within the Arkani-Hamed-Dimopoulos-Dvali framework, while constraints for curvature or brane separation are derived within the Randall-Sundrum framework. Based on the molecular spectroscopy of D2 molecules and HD+ ions, the compactification size for seven extra dimensions (in connection to M-theory defined in 11 dimensions) of equal size is shown to be limited to . While limits on compactification sizes of extra dimensions based on other branches of physics are compared, the prospect of further tightening constraints from the molecular method is discussed.