Coherent energy transfer is a highly efficient energy transfer pathway in photosynthesis. Matching of long-lived quantum coherence to the time scale of energy transfer is a prerequisite1–3. In contrast to short-lived electronic coherence4, the presence of excitonic-vibronic coherence in photosynthetic systems5,6 can account for the observed long-lasting quantum coherence. However, uncovering the mechanism of such coherence within a biological environment is challenging because of the presence of noise typically encountered at room temperature. This paper presents conclusive evidence of the existence of long-lasting electronic vibronic coherence in the allophycocyanin trimer, in which pigment pairs behave as excitonic dimers after photo-excitation. Employing ultrafast two-dimensional electronic spectroscopy, our study demonstrates an extension of the electronic-vibronic coherence time within the trimer compared with the isolated pigments. The prolonged quantum coherences were identified as arising from the quantum phase synchronization of the resonant vibrational collective modes for the pigment pair. The anti-symmetric resonant collective modes undergo fast energy dissipation when coupled to the delocalized electronic states of fast dephasing, while the decoupled symmetric resonant collective modes survive, exhibiting significantly lowered energy dissipation and supporting long-lasting quantum coherences. The presence of the quantum phase synchronization was confirmed by two experimental indicators consistent with the expectation. This paper provides empirical evidence revealing how biological systems effectively employ a quantum synchronization strategy to uphold persistent coherences, and our findings pave the way for protecting coherences against the noisy environment in quantum biology7.