In the Antarctic krill industry that develops rapidly in recent years, fishing and processing on the krill vessel has become an important link in the industry chain. Due to the biological characteristics of Antarctic krill, the fishing and processing production line has a direct impact on the product quality on vessel, and therefore affects the quality level of deep-processed products on land at the back end. The production lines of frozen shrimp, shrimp meat and shrimp powder processed intelligently on “Deep Blue” Antarctic krill shipping and processing vessel were taken as the research object to compare with traditional onboard processing, decompose their process flow and analyze the hazards based on HACCP system, and determine the critical control points;. The features of onboard Antarctic krill fishing and processing production line in the system were studied by preliminarily establishing the control system. This study shows that, with high automation, overall consistency and closure, the fishing and processing system reduced the probability of human and environment hazard, made the critical control points clearer, including all external inputs, parameter setting in control system and metal detecting, and had higher requirements for the implementation of GMP and SSOP and for the equipment maintenance and daily cleaning. The results could provide reference for the design and the establishment of onboard processing lines on other similar vessels.