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In this work, we showcase applications of single-molecule Fano resonance (SMFR) measurements beyond the determination of molecular excitonic energy and associated dipole orientation. We use the SMFR measurement to probe the local influence of a man-made single chlorine vacancy on the molecular transition of a single zinc phthalocyanine, which clearly reveals the lifting-up of the double degeneracy of the excited states due to defect-induced configurational changes. Furthermore, time-trace SMFR measurements at different excitation voltages are used to track the tautomerization process in a free-base phthalocyanine. Different behaviors in switching between two inner-hydrogen configurations are observed with decreasing voltages, which helps to reveal the underlying tautomerization mechanism involving both the molecular electronic excited states and vibrational excited states in the ground state.