In this article, we report on the characterization of various molecular junctions' current–voltage characteristics (I –V curves) evolution under mechanical modulations, by employing a novel electrochemically assisted-mechanically controllable break junction (EC-MCBJ) method. For 1, 4-benzenedithiol, the I –V curves measured at constant electrode pair separation show excellent reproducibility, indicating the feasibility of our EC-MCBJ method for fabricating molecular junctions. For ferrocene-bisvinylphenylmethyl dithiol (Fc-VPM), an anomalous type of I –V curve was observed by the particular control over the stepping motor. This phenomenon is rationalized assuming a model of atomic contact evolution with the presence of molecular junctions. To test this hypothesized model, a molecule with a longer length, 1, 3-butadiyne-linked dinuclear ruthenium(Ⅱ) complex (Ru-1), was implemented, and the I –V curve evolution was investigated under similar circumstances. Compared with Fc-VPM, the observed I –V curves show close analogy and minor differences, and both of them fit the hypothesized model well.