Exploring the charge transport process in molecular junctions is essential to the development of molecular electronics. Here, we investigate the temperature-dependent charge transport mechanism of carbon electrode-diarylethene single-molecule junctions, which possess photocontrollable molecular orbital energy levels due to reversible photoisomerization of individual diarylethenes between open and closed conformations. Both the experimental results and theoretical calculations consistently demonstrate that the vibronic coupling (thermally activated at the proper temperature) drives the transition of charge transport in the junctions from coherent tunneling to incoherent transport. Due to the subtle electron-phonon coupling effect, incoherent transport in the junctions proves to have different activation energies, depending on the photoswitchable molecular energy levels of two different conformations. These results improve fundamental understanding of charge transport mechanisms in molecular junctions and should lead to the rapid development of functional molecular devices toward practical applications.