Recently, better understanding of nano-area is required for 5 nm or less technology node. In particular, the high contact resistance generated in a nano-area significantly degrades the device performance. In this study, we propose a direct contact resistance measurement method without a test structure by separate processes to improve the nano-area contact resistance. The nano-area contact resistance of Ti-Ti and Cu-Cu decreased from 6.46 MΩ to 1.08 MΩ and from 3.78 MΩ to 1.48 MΩ, respectively, when the metal line and native layer formed on the surface were removed. In addition, it is confirmed that the contact resistance decreased with an increase in bonding strength in the case of nano-area homo-metal contact. However, the contact resistance is affected by the tunneling effect and bond energy according to the distance between the first layers of atoms in the case of nano-area hetero-metal contact.