Heat treatment reduces the quality of Antarctic krill (Euphausia superba), thus greatly limiting its industrial application. Although L-Lys immersion pretreatment can effectively improve the quality of heat-treated Antarctic krill meat, the underlying mechanism is unclear. This study aimed to investigate the effect of different L-Lys concentrations (0, 25, 50, 100, and 200 mM) on the aggregation behavior and structure of Antarctic krill myofibrillar protein solution before and after heat treatment. Compared with the untreated group, L-Lys decreased the surface hydrophobicity and particle size of the heat-treated Antarctic krill protein by 2.38 times and 18.27 times while increasing the solubility by 3.59 times. Furthermore, L-Lys intervention inhibited the formation of disulfide bonds in myofibrillar protein of the heat-treated Antarctic krill, enhanced the intermolecular hydrogen bonding force, improved the orderliness of the secondary structure, and "exposed" the tyrosine residues of the protein molecule. As a result, the polarity of the microenvironment was enhanced while the tertiary structure of the protein was altered, thus inhibiting thermal aggregation behavior and improving the water-holding capacity and tenderness of heat-treated Antarctic krill. This study reveals the mechanism of L-Lys inhibition of thermal aggregation behavior of Antarctic krill myofibrillar protein. Our results provide insights into the development and utilization of Antarctic krill protein in the food industry.