Pump-probe measurements by ultrashort THz pulses can be used to excite and follow the coherence dynamics in the time domain of single hydrogen molecules (H2) in the junction of a scanning tunneling microscope (STM). By tailoring the resonance frequency through the sample bias, we identified two spectral signatures of the interactions among multiple H2 molecules. First, the avoided level crossing featured by energy gaps ranging from 20 to 80 GHz was observed because of the level repulsion between two H2 molecules. Second, the tip can sense the signal of H2 outside the junction through the projective measurement on the H2 inside the junction, owing to the entangled states created through the interactions. A dipolar-type interaction was integrated into the tunneling two-level system model of H2, enabling accurate reproduction of the observed behaviors. Our results obtained by the quantum superposition microscope reveal the intricate quantum mechanical interplay among H2 molecules and additionally provide a 2D platform to investigate unresolved questions of amorphous materials.