Apostichopus japonicus is an economically pivotal cultivated sea cucumber in China. The prevalent “northern seedling breeding and southern grow-out” aquaculture model has established three core cultivation regions: Liaoning, Shandong and Fujian. Nevertheless, systematic comparisons of its nutritional quality and metabolic traits across these regions remain inadequate. This study investigated seasonal (spring and autumn) variations in the proximal nutrients, functional components (polysaccharides, saponins, phospholipids), amino acids, minerals and fatty acids in the body wall of A. japonicus sampled from the three regions via standard national and industrial protocols. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics was further applied to profile small-molecule metabolite disparities and unravel the molecular mechanisms linking geographical environments to nutrient accumulation and metabolic regulation.

Significant regional, seasonal and aquacultural differences in nutritional profiles were identified. Xiapu (Fujian) samples possessed high crude protein (40.82%), crude fat (3.76%) and saponin (1.2 mg/g) levels. Northern sea cucumbers accumulated markedly higher polysaccharides and total sugars, with Dalijia (Liaoning) samples showing the highest polysaccharide content (104.12 mg/g). Across all regions, spring samples exhibited superior amino acid nutritional quality with higher amino acid score, chemical score and essential amino acid index than autumn samples, and Xiapu samples had the highest lysine amino acid score (0.90).

Distinct mineral and fatty acid profiles were observed among samples. Rongcheng autumn samples had rich magnesium (13.53 g/kg) and iron (327.33 mg/kg); Penglai spring samples contained the highest calcium (11.70 g/kg), magnesium (14.07 g/kg) and sodium (112.33 g/kg), while Xiapu samples were richest in potassium (9.59 g/kg) and zinc (25.10 mg/kg). Additionally, Xiapu samples had significantly higher total polyunsaturated fatty acids and EPA+DHA content (24.95%) than northern counterparts.

Metabolomics analysis revealed clear north-south metabolic differentiation. Xiapu and northern samples exhibited completely distinct metabolic profiles, with differential pathways concentrated in ABC transporters, nucleotide metabolism, and vitamin digestion and absorption. Northern samples also showed intra-regional metabolic divergence, and Dalijia and Wendeng samples shared closer metabolic characteristics. Key differential metabolites including leucine butyl ester and 6-tuliposide A were screened as potential traceability markers. This study clarifies the geographical nutritional and metabolic characteristics of cultivated A. japonicus, providing scientific support for its origin traceability, quality grading, aquaculture optimization and functional food development.