The surface structure and electrochemical behavior of self-assembled monolayers (SAMs) prepared from benzenethiol (BT), cyclohexanethiol (CHT), and cyclopentanethiol (CPT) on Au(111) surface were examined by scanning tunneling microscopy (STM) and cyclic voltammetry (CV) to understand the influence of thiol molecular backbone structure on the formation and reductive desorption behavior of SAMs. STM imaging showed that BT and CPT SAMs on Au(111) surface formed at room temperature were mainly composed of disordered domains, whereas CHT SAMs were composed of well-ordered domains with three orientations. From these STM results, we suggest that molecule-substrate interaction is a key parameter for determining the structural order and disorder of simple aromatic and alicyclic thiol SAMs on Au(111). In addition, the reductive desorption peak potential for BT SAMs with aromatic rings was observed at a less negative potential of -566 mV compared to CHT SAMs (-779 mV) or CPT SAMs (-775 mV) with aliphatic cyclic rings. This reductive desorption behavior for BT SAMs is due to the presence of p-orbitals on the aromatic rings, which promote facile electron transfer from the Au electrode to BT as compared to CHT and CPT. We also confirmed that the reductive desorption behavior for simple alicyclic thiol SAMs such as CHT and CPT SAMs on Au electrodes was not significantly influenced by the degree of structural order.