Headspace solid-phase microextraction, combined with gas chromatography–mass spectrometry and partial least squares discriminant analysis, was adopted to study the rule of change in volatile organic compounds (VOCs) for domestic and imported fishmeal during storage with different freshness grades. The results showed that 318 kinds of VOCs were detected in domestic fishmeal, while 194 VOCs were detected in imported fishmeal. The total relative content of VOCs increased with storage time, among which acids and nitrogen-containing compounds increased significantly, esters and ketones increased slightly, and phenolic and ether compounds were detected only in domestic fishmeal. Regarding the volatile base nitrogen, acid value, pH value, and mold counts as freshness indexes, the freshness indexes were significantly correlated with nine kinds of VOCs (p < 0.05) through the correlation analysis. Among them, volatile base nitrogen had a significant correlation with VOCs containing nitrogen, acid value with VOCs containing carboxyl group and hydrocarbons, pH value with acids which could be used to adjust pH value, and mold counts with part of acids adjusting pH value and VOCs containing nitrogen. Due to the fact that the value of all freshness indexes increased with freshness degradation during storage, based on volatile base nitrogen and acid value, the fishmeal was divided into three freshness grades, superior freshness, corrupting, and completely corrupted. By using partial least squares discriminant analysis, this study revealed the differences in flavor of the domestic and imported fishmeal during storage with different freshness grades, and it identified four common characteristic VOCs, namely ethoxyquinoline, 6,7,8,9-tetrahydro-3H-benzo[e]indole-1,2-dione, hexadecanoic acid, and heptadecane, produced by the fishmeal samples during storage, as well as the characteristic VOCs of fishmeal at each freshness grade.