We present here a systematic theoretical study on the effect of Duschinsky rotation on charge transport properties of molecular junctions in the sequential tunneling regime. In the simulations we assume that only two electronic charging states each coupled to a two dimensional vibrational potential energy surface (PES) are involved in the transport process. The Duschinsky rotation effect is accounted by varying the rotational angle between the two sets of displaced PESs. Both harmonic potential and anharmonic Morse potential have been considered for the cases of the intermediate to strong electron–vibration couplings. Our calculations show that the inclusion of the Duschinsky rotation effect can significantly change the charge transport properties of a molecular junction. Such an effect makes the otherwise symmetric Coulomb diamond become asymmetric in harmonic potentials. Depending on the angle of the rotation, the low bias current could be significantly suppressed or enhanced. This effect is particularly prominent in the Franck–Condon (FC) blockade regime where the electron–vibration coupling is strong. These changes are caused by the variation of the FC factors which are closely related to the rotational angle between the two sets of PESs involved in the charge transport process. For a molecular junction with Morse potentials, the changes caused by Duschinsky rotation are much more complicated. Both the amplitude and shape of the Coulomb diamond are closely dependent on the rotational angle in the whole range from 0 to 2π. One interesting result is that with a rotation angle of π (and also π/2 for certain cases) symmetric Coulomb diamonds can even be formed from the intrinsically asymmetric Morse potential. These results could be important for the interpretation of experimental observations.