Two odorless, water-soluble exopolysaccharide (EPS) fractions, EPS-1 and EPS-2, were isolated from a newly isolated Bacillus amyloliquefaciens strain C-1 and purified by ion exchange and gel chromatography. The purified EPS-1 contained glucose/mannose/galactose/arabinose in a relative proportion of 15:4:2:1, and possessed a molecular weight of 79.6 kDa, while EPS-2 contained only glucose and mannose in a 3:1 ratio, with the molecular weights of 19.8 kDa. The antioxidant activity results showed that EPS-1 exhibited strong reducing power, superoxide radicals (O(2-)·), and hydroxyl free radicals (OH·) scavenging activities. For the H2O2-induced injury in HepG2 cells, EPS-1 significantly decreased the formation of reactive oxygen species, intracellular malondialdehyde levels, and restored intracellular superoxide dismutase activity. For EPS-2, there had no detectable antioxidant activities. And all these results collectively showed that as a natural antioxidant, only EPS-1 produced by C-1 had considerable potential to be used as medical compounds or functional additives.