The invention discloses a method for cleaning a ship pipeline and relates to the field of a ship manufacturing technology; pipes required for being cleaned are connected into a pipeline from the head to the tail, wherein a pipeline vibrator is arranged outside the pipeline which is pre-purged by accessing compressed air, the pipe vibration is started, both ends of the pre-purged pipeline are connected with a ship pipeline cleaning device, a hydraulic pump begins to operate after a motor is started, and a heater in an oil tank is started to control fuel temperature; the pipeline begins to hydraulically clean, within initial 8 hours, the pulse function is started for 2 hours by spacing 2 hours and backwashed for 1 hour by spacing 1 hour in the cleaning process, after 8 hours, the hydraulic oil is detected, the hydraulic pump stops working after the detected oil pollution level reaches the standard; when nitrogen is accessed into a nitrogen input end, the residual hydraulic oil in the cleaning pipeline is blown out, and the pipeline cleaning process is finished. The method can solve the problem that a ship hydraulic pressure system is faulted because the ship pipeline isn't thoroughly cleaned in the existing technology.