Generally, a low damping system has a small phase margin. One should deal with the problems of long time delay and unmodeled dynamics for active vibration control of a low damping system sometimes. For a pneumatic drive flexible manipulator system, time delay or phase lag and unmodeled nonlinear dynamics problems have raised the level of concern. It is vital but difficult to regulate the phase of vibration controller, to compensate for the time-varying phase lag or time delay due to the gas compression and parametric uncertainty of the pneumatic control system. The objective of this investigation is to formulate an active vibration control law with practical approach of phase adjusting for a pneumatic drive flexible manipulator system. A control strategy named adaptive phase adjusting control is designed and applied. The adaptive phase adjusting controller is implemented by using the phase angles as explicit parameters. These parameters are tuned online, depending on the corresponding control performance index. To evaluate the control performance of the designed adaptive phase adjusting technique, experiments are conducted on a pneumatic drive flexible manipulator experimental setup. The experimental results demonstrate the adaptive phase adjusting controller has the ability to optimize the phase angle accordingly. Vibration suppression is accomplished by using the designed adaptive phase adjusting controller, even with time delay and unmodeled dynamics in the system.