The invention discloses a comprehensive aquatic product processing leftover utilization method which comprises the following steps: with processing leftovers of crustacean including fish, shrimp, crab and the like as the raw materials, cleaning, low-temperature drying, cryogenic grinding, complex enzymatic degradation, organic acid extraction, high-speed centrifugal separation, reverse osmosis dehydration, molecule embedding, high-pressure homogenizing, vacuum low-temperature cryogenic drying, pelletizing, tabletting, automatic bottled packaging production line processing and outer packing are carried out, and all high value-added bio-active substances including astaxanthin, protein, organic calcium, chitin and the derivative of the chitin namely chitosan in the aquatic product processing leftovers are extracted, so that resources are comprehensively and effectively utilized without waste discharge. According to the invention, the moderate bio-enzyme degradation technique is adopted, the whole process is carried out under the low-temperature condition, strong acid, strong base and toxic solvents are not used, the technological process is short, the industrial chain is long, and the products are high in bioactivity, various in variety, excellent in quality, safe to eat, wide in application fields, large in potential market, and high in comprehensive economic benefit.