The invention discloses a magnetic droplet accelerator and an operating method thereof, which relate to the field of droplet dynamics. The magnetic droplet accelerator comprises a droplet generator, alaser signal acquisition device, a solenoid, a coil gun module and a controller, wherein a magnetic liquid generated by the droplet generator drops into the solenoid from right above the solenoid, the laser signal acquisition device is arranged at an inlet of the solenoid, that is, where a droplet is about to fall into the solenoid, the coil gun module is connected with the solenoid and suppliespower to the solenoid, and the coil gun module and the laser signal acquisition device are each connected with the controller. The magnetic droplet accelerator occupies a small space and is convenientin placement and arrangement. The magnetic droplet accelerator accelerates the magnetic droplet by adopting a coil gun principle, and further controls acceleration of the droplet through changing anoutput voltage of a boosting module in the coil gun module, so as to achieve the purpose of controlling the droplet velocity. According to the magnetic droplet accelerator and the operating method thereof, the adjustable range of droplet acceleration is large, and the droplet is accelerated stably.