This paper proposes the bilateral control method for a pair of manipulators which have different structures considering the fluctuation of an equivalent mass matrix. Bilateral control is one of the methods that controls position and force bidirectionally between two actuators. By using this method, operators can get haptic sensation from the remote environment during teleoperation. When considering the practical situation, the desired structure of robots would be different between the operator and remote sides depending on a task or environment. Therefore, bilateral control between two manipulators with different structure needs to be considered. In the method using Workspace Observer (WOB), conventionally, the nominal value is used for the equivalent mass matrix. However, an error occurs between the nominal and true values of equivalent mass matrix, and this error deteriorates the stability or noise-sensitivity of the system. In addition, it deteriorates the accuracy of the force estimation since Workspace Reaction Force Observer (WRFOB) estimates external force including this error. To overcome this problem, the control system needs to be designed based on the equivalent mass, which fluctuates depending on the posture of manipulators. By using the estimated equivalent mass matrix for WOB, the mass fluctuation can be considered, however, the interference between position control and force control occurs as the equivalent mass is different between the master and slave. Therefore, in the proposed method, Modal space Disturbance Observer (MDOB) with estimated task mass matrix is used to reduce the interference. Experiments were conducted to validate the proposed method.