Molecular dynamics of hydrogen molecules (H2) on surfaces and their interactions with other molecules have been studied with the goal of improvement of hydrogen storage devices for energy applications. Recently, the dynamic behavior of a H2at low temperature has been utilized in scanning tunnelling microscopy (STM) for sub-atomic resolution imaging within a single molecule. In this work, we have investigated the intermolecular interaction between H2and individual vanadyl phthalocyanine (VOPc) molecules on Au(111) substrates by using STM and non-contact atomic force microscopy (NC-AFM). We measured tunnelling spectra and random telegraphic noise (RTN) on VOPc molecules to reveal the origin of the dynamic behavior of the H2. The tunnelling spectra show switching between two states with different tunnelling conductance as a function of sample bias voltage and RTN is measured near transition voltage between the two states. The spatial variation of the RTN indicates that the two-state fluctuation is dependent on the atomic-scale interaction of H2with the VOPc molecule. Density functional theory calculations show that a H2molecule can be trapped by a combination of a tip-induced electrostatic potential well and the potential formed by a VOPc underneath. We suggest the origin of the two-state noise as transition of H2between minima in these potentials with barrier height of 20-30 meV. In addition, the bias dependent AFM images verify that H2can be trapped and released at the tip-sample junction.