This study presents a comparative analysis of the structure–bioactivity relationship of fucoidans extracted from five brown seaweeds. Comprehensive characterization (HPLC-SEC, HPAEC-PAD, FTIR, and NMR, etc.), revealed distinct molecular weights (75–1180 kDa) and sulfate content (16–46 %). A key finding was the potent bioactivity of low molecular weight fucoidan from Macrocystis pyrifera (F5B, 75 kDa), which demonstrated anticoagulant activity, and significantly enhanced macrophage proliferation (187 ± 27 %, p < 0.0001). Most notably, F5B provided exceptional cytoprotection against UV-induced damage, significantly reducing cell membrane injury as measured by LDH release (76.1 ± 5.5 % vs. control, p = 0.0032). In contrast, Alaria esculenta fucoidan (F4A) most effectively stimulated fibroblast proliferation and migration (128 ± 7.7 %, p < 0.05), upregulating key repair markers, including TGF-β1 and collagen I. Laminaria hyperborea (F2B) improved keratinocyte migration, upregulated IL-8, and downregulated TNF-α. LC-MS metabolomic analysis revealed that fucoidan treatment altered intracellular sugar metabolites associated with cytoprotective effects. Although F5B-treated cells exhibited lower fructose levels, this likely reflects increased metabolic utilization linked to enhanced cytoprotection against UV-B–induced damage. Cladosiphon okamuranus fucoidan (F3B) specifically enhanced phagocytosis (131.5 ± 1.6 %, p < 0.0001). Overall, this study established a clear link between fucoidan structure and biological function, identifying M. pyrifera fucoidan as a promising candidate for immunomodulation and UV protection, while A. esculenta fucoidan demonstrates strong potential for promoting tissue repair.