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This study aimed to investigate the effect of temperature and time changes in two typical thermal processing procedures, frying and baking, on squid quality. Increasing the frying/baking temperature and prolonging the time significantly impacted color, L* value decreased over time, and a* value increased (P < 0.05). Total nitrogen, non-protein nitrogen, and cadaverine levels increased significantly after thermal process (P < 0.05), whereas histamine levels increased and subsequently reduced, which was attributed to the process of lipid oxidation. The concentration of pyrazine was dramatically increased (fried: 3.01 ∼ 1468.27 µg/kg; baked: 0.00 ∼ 836.14 µg/kg). The hierarchical cluster analysis was applied to analyze the complicated raw data of squid in order to evaluate the quality under different frying/baking conditions. Squid, whether fried or baked, took on a deeper color, contained more protein per unit weight, and tasted more desirable, although the histamine levels rose at certain temperatures as well. This study indicated the appropriate cooking methods and conditions could help to preserve nutrition while keeping histamine levels under control.