The invention, which belongs to the measuring method technology field, relates to a real-time difference measuring apparatus for a regular moving boat-carrying base station and a working method thereof. According to the method, on the condition of a static state of a boat-carrying GNSS base station, a long-time positioning operation is carried out and an accurate initial position of the base station is obtained; a moving regularity of the boat-carrying GNSS base station is determined according to a position relation of between a target working area of the boat-carrying GNSS base station and atarget working area of an RTK flow station; and at the same time, an observation speed, a predetermined speed and driving time of the base station are processed, a track error of the base station is calculated and decided, and a driving state of the boat-carrying GNSS base station is also adjusted. In the case of determination of a speed and a starting position of a course of the boat-carrying GNSS base station, an accurate and real-time position of the boat-carrying GNSS base station can be obtained; and a carrier phase difference operation is carried out on range information, carrier information, and navigation message information of the boat-carrying GNSS base station so as to obtain a difference correction number; the difference correction number is sent to the RTK flow station by a data link unit, so that real-time difference measurement of the regular moving boat-carrying base station is completed.