The present invention provides a dredged soil transport system including a pipe module wound with a coil applying an electromagnetic field to an internally flowing dredged soil and including a plurality of pipelines, a pump module configured to provide a transport pressure for transport of dredged soil to the pipe module, database stored with flow information on flow velocity and flow form in response to physical properties of liquefied unit, and a control module communicating with the pipe module, the pump module and the database wiredly and wirelessly and applying, to the coil, a current of waveform matching to a flow waveform of the dredged soil transported inside the pipeline, and a control method thereof.