The invention provides an automatic plotting system for navigation radar. The system comprises a log, a compass, a GPS, an AIS, a radar data acquisition processing card, a transceiver unit, an industrial computer, and a control unit, wherein the log, the compass, the radar antenna transceiving unit, the AIS and the GPS are connected with the radar data acquisition processing card; the radar data acquisition processing card is inserted in a PCI slot of the industrial computer, and is in charge of receiving information transmitted by the log, the transceiver unit, the compass and the GPS, converts the information into digital information, and transmits the information to the industrial computer; the industrial computer marks a target for a radar digital signal which is transmitted by the radar according to the data acquisition processing card to acquire an accurate position of the target, and transmits the result to a display; and the control unit is connected with the industrial computer. The automatic plotting system has low cost, stable and reliable system performance and convenient maintenance.