Previous studies showed that crude Houttuynia cordata polysaccharides (CHCP) exerted therapeutic effects on acute lung injury induced by influenza A virus (IAV) in mice. Here, an acidic heteropolysaccharide from H. cordata, named HCPM (Mw, 19.1 kDa), was obtained directly from CHCP using sequential ultrafiltration membrane columns. The backbone of HCPM was consisted of 1, 3, 6-β-Manp, 1, 4-α-GalpA, 1, 2-α-Rhap, and 1, 2, 4-α-Rhap, with main branches of glucan, arabinan, and galactan substituted at C-3 of 1, 3, 6-β-Manp or C-4 of 1, 2, 4-α-Rhap. The structural information was further validated by oligosaccharide sequencing analysis using UPLC-ESI-MS. Furthermore, HCPM exhibited a potent anti-complementary activity with CH₅₀ value of 254.1 ± 7.8 μg/mL in vitro and significantly attenuated IAV-induced lung and gut injuries in vivo by inhibiting viral replication, reducing inflammatory responses, and suppressing complement overactivation. These results suggested that HCPM might be a key H. cordata substance for pulmonary infection treatment.