The dynamics of bulk material usually appears as continuous variation because of the group effect. But, for a single two-level system, its dynamics behaves as stochastic switching driven by tunneling effect or external quantum noise. In this dissertation, we present the dynamics of a single molecule stochastically switching between two conformational states studied with scanning tunneling microscope (STM). Such switching dynamics is jointly driven by the inter-state tunneling and inelastic electron tunneling. We mainly studied the stochastic switching interacting with different types of periodic drive, photon and inelastic tunneling electrons. By monitoring the DC, first harmonic and second harmonic response of the system, we discovered many interesting phenomena at single molecule level: frequency dependent stochastic rectification, dynamic response of optical rectification, and dynamic response of inelastic electrons tunneling spectroscopy. Our numerical solutions to the master differential equations agree with the experimental results. In addition, we also constructed models based on different approximation to interpret the physical meaning of experimental results.We achieved many technical advancements during the experimental investigation: inventing a Z-compensation method to solve the thermal effect induced by laser chopping, inventing the pulse count method to measure the single molecule switching rate across seven orders of magnitude, and implementing a constant amplitude rectification frequency scan at the tunneling junction. Our study deepens the understanding of the stochastic behavior of quantum system and expands the scope and capability of single molecule spectroscopy, such as measuring sub-picosecond relaxation and full range optical spectroscopy.