A high contact resistance restricts the application of carbon nanotubes (CNTs) in fabrication of field-effect transistors (FETs). Thus, it is important to decrease the contact resistance and investigate the critical influence factors such as the contact length and contact force. This study uses nanomanipulation to characterize both the resistance and the force at a CNT/Au side-contact interface inside a scanning electron microscopy (SEM). Two-terminal CNT manipulation methods, and models for calculating the resistance and force at contact area, are proposed to guide the measurement experiments of a total resistance and a cantilever's elastic deformation. The experimental results suggest that the contact resistance of CNT/Au interface is large (189.5 kΩ) when the van der Waals force (282.1 nN) dominates the contact force at the interface. Electron-beam-induced deposition (EBID) is then carried out to decrease the contact resistance. After depositing seven EBID points, the resistance is decreased to 7.5 kΩ, and the force increases to 1339.8 nN at least. The resistance and force at the contact area where CNT was fixed exhibit a negative exponential correlation before and after EBID. The good agreement of this correlation with previous reports validates the proposed robotic system and methods for characterizing the contact resistance and force.