The invention discloses a compression device for storing and transporting media in a box and a compression method thereof. The compression device of the invention comprises a medium conveyor, a compression main body, a pressure head mechanism, an actuator, a box conveyor and a control module, wherein , the indenter mechanism and the actuator are respectively connected with the compression main body, the indenter mechanism, the actuator and the box conveyor are respectively electrically connected with the control module, the box conveyor is placed and conveyed the box, the box includes the box compartment, the compression main body Including a frame and a compression chamber, the compression chamber is installed on the frame, and the compression chamber and the box chamber are arranged adjacent to each other, the medium enters the compression chamber through the medium conveyor, and the pressure head mechanism reciprocates between the compression chamber and the box chamber to transfer the medium. Push from the compression compartment to the box compartment. The compressing device for storing and transporting medium in the box and the compressing method thereof of the present invention focus on compressing a large amount of pulverized medium, carry out fully automatic operation, reduce personnel input, improve efficiency and increase benefit.