An advanced understanding of the molecule–electrode contact interfaces of single-molecule junctions is a necessity for real world application of future single-molecule devices. This study aims to elucidate the change in the contact tunnelling barrier induced by junction extension and how this change affects the resulting junction conductance. The contact barrier of Au–octanedithiol/octanediamine–Au junctions was studied under triangle (TRI) mechanical modulations using the modified scanning tunneling microscopy (STM) break junction technique. The experimental results reveal that as the junction separation extends, the contact barrier of octanedithiol follows a unique trend, a linear increase followed by a plateau in barrier height, which is in contrast to that of octanediamine, a nearly rectangle barrier. We propose a modified contact barrier model for the unique barrier shape of octanedithiol, based on which the calculation agrees well with the experimental data. This study shows unprecedented experimental features of the molecule–electrode contact barrier of single-molecule junctions and provides new insights into the nature of contact effect in determining electron transport through single-molecule junctions.