Molecular junctions hold great potential for future microelectronics, while the practical utilization has long been limited by the problem of conformational deformation during charge transport. Here we present a first-principles theoretical study on the surface-enhanced Raman spectroscopy (SERS) characterization of the p-terphenyl-4,4 ''-dithiol molecule and its 2,2',5',2 ''-tetramethylated analogue in gold junctions to investigate the molecular deformation mechanism. The effects of charge injection and external electric field were examined, both of which could change pi-conjugation by varying the dihedral angle between the central and ending rings (D-IPT). The induced significant structural deformations then change SERS responses. Only the SERS responses under an external electric field can account for the experimentally observed Raman spectra, and those of charge injections cannot. Moreover, applying a strong electric field could enlarge the conductivities of the two molecular junctions, agreeing well with experiments. This information not only elaborates that the electric field effect constitutes one important mechanism for molecular deformation but also provides useful insights for the control of charge transport in molecular junctions.