Three water-soluble polysaccharides (UPPs 1–3) were obtained from edible green alga Ulva pertusa. The chemico-physical analyses indicated that UPPs 1–3 possessed molecular weights of 376.7 kDa, 57.21 kDa, and 131.13 kDa, with sulfate contents of 26.01 ± 8.13%, 9.86 ± 3.24%, and 13.32 ± 6.56%, respectively, and composed of arabinose, galactose, glucose, xylose, galacturonic acid, glucuronic acid, and mannuronic acid, with different ratios. The in vitro studies revealed that UPP-1 showed significant effects on the proliferation and phagocytic activity of macrophage, release of nitric oxide, and secretion of cytokines (TNF-α and IL-6). The transcript-metabolite analysis of UPP-1 treated macrophage revealed 4747 differential genes (2416 up-regulated and 2331 down-regulated) and 94 differential metabolites (77 up-regulated and 17 down-regulated) that significantly co-mapped a transcript-metabolite correlation network of biosynthesis of amino acids, glycerophospholipid metabolism, and carbon metabolism. Thus, these findings provide a valuable foundation for the potential application of U. pertusa polysaccharides.