Abstract: Jellyfish is rich in collagen, high in water content, perishable, and commonly used salt and alum treatment to make salted jellyfish, resulting in excessive aluminum content. Chlorogenic acid (CGA) solution was used to reduce the aluminum content in jellyfish for decreasing the residual amount of aluminum in jellyfish and reducing the damage of aluminum to the human body. The effect of CGA on the structure of collagen in jellyfish was explored through ultraviolet spectrophotometry, thermal analysis, molecular docking, and molecular dynamics simulation. The results showed that CGA significantly reduced the residual amount of aluminum in salted jellyfish. When the concentration of CGA was 0.2 mg/mL, the removal amount of aluminum was the highest, and the removal rate was 51.51%. At the same time, the hardness, chewiness, and resilience of salted jellyfish were improved, and CGA maintained the integrity of the microstructure of salted jellyfish. CGA increased the relative content of α-helix in jellyfish collagen from 33.63% to a maximum of 39.12%, decreased the relative content of β-fold, β-turn, and random curl, and improved the thermal stability of jellyfish collagen. The collagen interacted with CGA through hydrogen bonding and hydrophobic interaction, and the collagen and CGA formed a stable complex. This study enriched the dealumination technology of salted jellyfish and provided a theoretical basis for the green processing of jellyfish.