System identification is an approach for parameter detection and mathematical model determination using response signals of a dynamic system. Two degrees of freedom (2DOF) pendulum controlled by a QUBE-servo motor is a great experiment device to work with; though it is not easy to control this system due to its complex structure and multi-dimensional outputs. Hence, system identification is required for this system to analyze and evaluate its dynamic behaviors. This paper presents a methodology for identifying a 2DOF pendulum and its dynamic behaviors including noise from an encoder cable. Firstly, all parameters from both mechanical and electrical sides of the QUBE-servo motor are analyzed. Secondly, a mathematical model and identified parameters for the 2DOF pendulum are illustrated. Finally, disturbances from encoder cable of the QUBE-servo motor which introduce an unwanted oscillation or self-vibration in this system are introduced. The effect of itself on output response signals of the 2DOF QUBE-pendulum is also discussed. All identified parameters are checked and verified by a comparison between a theoretical simulation and experimental results. It is found that the disturbance from encoder cable of the 2DOF QUBE-pendulum is not negligible and should be carefully considered as a certain factor affecting response of system.