The invention relates to a method of comprehensive utilization and processing of puffer fish. Firstly, puffer fish is cleaned and treated to remove the blood, and then fish fins, the mouth, the skin, the eyes, the gill and the viscera are cut off, thereby implementing external treatment. Secondly, the head, the viscera, the body and the bone of the puffer fish are respectively treated, thereby implementing internal treatment. Further, the blood, the mucosa, the mucilage, the subcutaneous tissue, the fin, the eyes, the kidney, the heart, the gallbladder, the spleen, the stomach, the intestines, the mesentery, the bladder and the anus in the process are placed in a dish for inedible parts. Finally, the treated fins, skin, mouth, head, muscles, testicle and bones are placed in a dish for edible parts; and the ovary and the liver are placed in a dish for highly toxic parts. The method ensures the safety and sanitation of the puffer fish processed products to the greatest extent in methodology and process flow, ensures the safety and stability in the edibility of the puffer fish after long-term preservation, and realizes the comprehensive utilization of puffer fish resource.