This paper describes the anchoring group effect of molecular diodes on rectifying behavior. Two molecular diodes with different anchoring groups, which are based on diblock co-oligomeric structures, have been synthesized and characterized. Scanning tunneling spectroscopy (STS) measurements revealed the correlation of rectifying effects in these molecular diodes with anchoring groups such as thiol and isocyanide. The combination of theoretical calculation and experimental results on these molecular diodes demonstrated that the rectifying effect could be affected by the nature of anchoring groups due to the bond dipoles at the interface and internal polarization inside the molecules.