To explore bioactive polysaccharides from the byproducts of squid processing, a heteropolysaccharide, named SV2-1, was isolated from the viscera of squid Ommastrephes bartrami by autolysis, anion-exchange and gel-permeation chromatography and measured for its neuroprotective activity. It was a homogeneous polysaccharide with a molecular weight of 2.3 kDa by HPSEC analysis. SV2-1 contained glucuronic acid, galactosamine and fucose in the ratio of 1.0:1.1:1.2. Its structural characteristics were elucidated by methylation analysis, gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR). The backbone of SV2-1 was composed of alternant →4)-α-l-Fucp-(1→ and →3)-β-d-GlcUA-(1→ Most of →4)-α-l-Fucp-(1→ (90%) was substituted by single α-d-GlcNAc as the branches. SV2-1 can protect against the death of PC12 induced by 6-OHDA, and effectively improves cell viability and reduces extracellular LDH release in PC12 cells after injury. Moreover, SV2-1 significantly increases SOD activity but decreases MDA levels.