The vibration of piping systems is one of the most important causes of accelerated equipment wear and reduced work efficiency and safety. In this study, an active vibration control method based on a fractional-order proportional–integral–derivative (PID) controller was proposed to suppress pipeline vibration and reduce pipeline damage. First, a mathematical model of the distributed piping system was established using the finite element analysis method, and the characteristics of the distributed piping system were studied effectively. Further, the time-frequency domain parameter identification method was used to realise the system identification of the cross-point vibration transfer function between the brake and sensor, and the particle swarm optimisation algorithm was utilised to further optimise the transfer function parameters to improve the system identification accuracy. Therefore, a fractional-order PID controller was designed using the D-decomposition method, and the optimal controller parameters were obtained. The experimental and numerical simulation results show that the improved system identification algorithm can significantly improve modelling accuracy. In addition, the designed fractional-order PID controller can effectively reduce the system’s overshoot, oscillation time, and adjustment time, thereby reducing the vibration response of piping systems.