The invention discloses an ultrasonic cutting method of a honeycomb core boss structure. The method is characterized by comprising following steps that S1, hole case end face finish machining; S2, outline forming machining; S3, cutting-up partitioning machining; S4, removal machining of an outer material of the honeycomb core boss structure; S5, honeycomb core boss structure ladder face finish machining. The traditional honeycomb core cutting machining manner is changed, the machining defects brought by traditional cutting are overcome, and the machining quality and the machining efficiency ofthe honeycomb core boss structure are improved.