In this article, we have investigated the influence of the nitro side-group on the single molecular conductance of pyridine-based molecules by scanning tunneling microscopy break junction. Single molecular conductance of 4,4′-bipyridine (BPY), 3-nitro-4-(pyridin-4-yl)pyridine (BPY-N), and 3-nitro-4-(3-nitropyridin-4-yl)pyridine (BPY-2N) were measured by contact with Au electrodes. For the BPY molecular junction, two sets of conductance were found with values around 10−3.1 G0 (high G) and 10−3.7 G0 (low G). The addition of nitro side-group(s) onto the pyridine ring resulted in lower conductance of 10−3.8 G0 for BPY-N and 10−3.9 G0 for BPY-2N, respectively, which can be attributed to the twist angle of two pyridine rings. Moreover, the steric hindrance of nitro group(s) also affects the contacting configuration of electrode-molecule-electrode. As a consequence, only one set of conductance value was observed for BPY-N and BPY-2N. Our work clearly shows the important role of side-groups on the electron transport of single-molecule junctions.