Rice (Oryza sativa L.) is a salt-sensitive crop which could be suppressed seriously by salt stress at germination stage. Some seaweeds polysaccharides could enhance plants resistance but there is little research about polysaccharides from Grateloupia filicina in agriculture. Therefore, G. filicina polysaccharide (GFP) and low molecular weight (MW) G. filicina polysaccharide (LGFP) were applied to rice seeds under salt stress (GFP: 2093.4 kDa, LGFP-1: 40.8 kDa, LGFP-2: 22.6 kDa, LGFP-3: 5.1 kDa, LGFP-4: 3.0 kDa). Relatively low MW polysaccharides LGFP1-4 showed better effect than GFP, and LGFP-1 showed the best effect on germination potential, germination index, shoot/root length and vigor index than negative control by 26.67, 14.27, 30.50, 202.65 and 162.78%, respectively. Optimum concentration was determined at 0.1 mg/mL, and LGFP-1 increased proline content, superoxide dismutase (SOD) and peroxidase activities (POD) which improved ability of osmotic adjustment and reactive oxygen species (ROS) scavenging. FITC-labeled LGFP-1 (F-LGFP-1) was to investigate the polysaccharide absorption and it was be observed in root and shoot with different distribution. Finally, expression of Na+/H+ antiporter gene was up regulated which suggested LGFP-1 could protect rice seeds by regulating Na+ content. This research showed potential application of polysaccharides from G. filicina for increasing rice seeds salt tolerance.