Chemical analysis showed that pH, b* values, myosin turbidity, carbonyl content, and surface hydrophobicity elevated in hooked, trawl‐net, and radar‐net hairtail (Trichiurus haumela, HH, TH, and RH) muscles with the prolonged cryopreservation time (‐18℃, 120 d). In contrast, L*, a* values, textural properties, and myosin solubility existed decreasing trends. Microstructural results showed that freezing resulted in disordered myofibrils, decreased collagen fibers, widened myofibrillar space, and increased fragmentation in hairtail muscles. Furthermore, volatile flavor analysis suggested that aldehydes, ketones, alcohols, and amines were the key factors for the overall flavor formation in hairtails during cold storage. Pearson correlation coefficient analysis revealed that the color, texture, and protein oxidation had close correlations with VOCs. Among the three different kinds of hairtail, fresh RH fillets exhibited an attractive aroma with high economic value, long‐term frozen TH muscle tissues were prone to deterioration in texture, microstructure, and flavor, and the HH samples presented stable quality characteristics and storage performance.