The observation of vibrational coherence has become significant because it reflects the spatial and temporal localization of a nucleus in a specific mode and characterizes energy flow and multiple kinetic relaxations in chemical dynamics. Vibrational coherence in the S1 state of 2,4-difluoroanisole has been investigated in real time by femtosecond time-resolved photoelectron spectroscopy and time-of-flight mass spectroscopy. Quantum beats of superpositions exhibit temporal oscillations with a frequency of 78 cm-1. Combining the structure computations, oscillations derive from the structure change from planar to nonplanar geometry, which correspond the coherence wavepackets moving from the Franck-Condon region toward the minimum point of the potential energy surface, elucidating the energy flows following the excitation of 2,4-difluoroanisole in the S1 state. The phases of the quantum beat via the resonant Rydberg states exhibit a shift of π rad. The vibrational coherent phase modulation via the resonant Rydberg states will facilitate the chemical coherence control in complex molecular systems.