Crisp biscuits are susceptible to lipid oxidation during storage, resulting in flavor deterioration and a decline in quality. To systematically investigate the dynamic changes in lipid oxidation indicators and their effect on product flavor, this study utilized headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) to analyze samples stored for 0, 6, 8, 10, 12, and 14 months. Monitoring of lipid oxidation indices revealed that the acid value (AV) and peroxide value (POV) increased significantly with storage time (P<0.05). In contrast, the oxidative stability index (OSI) decreased markedly (P<0.05), with a 34.47% reduction over 14 months. A total of 44 volatile compounds were identified, including aldehydes (9), ketones (8), acids (1), esters (8), alcohols (4), hydrocarbons (7), pyrazines (6), and others (1). Flavor profiling demonstrated significant temporal variations: aldehydes (e.g., hexanal, isovaleraldehyde), ketones (e.g., hydroxyacetone), and acids (e.g., acetic acid) increased significantly during storage (P<0.05), whereas esters (e.g., ethyl acetate) decreased sharply (P<0.05), with a 93.24% reduction by month 14. Multivariate statistical analyses, including partial least squares-discriminant analysis (PLS-DA) and principal component analysis (PCA), combined with variable importance in projection (VIP>1) and statistical significance (P<0.05), identified 13 key differential volatile markers. Further screening highlighted seven compounds—hexanal, isovaleraldehyde, hydroxyacetone, acetic acid, acetamide, acetylacetone, and 2-methyltetrahydrofuran-3-one—as core markers indicative of flavor deterioration and overall quality decline in crisp biscuits. Correlation analysis confirmed lipid oxidation as the primary driver of off-flavor development and quality degradation. These findings demonstrate that HS-SPME-GC-MS combined with multivariate analysis is an effective approach for identifying critical differential flavor compounds during storage, providing a scientific and methodological basis for early prediction and quality monitoring of crisp biscuits.