To compare the effects of different modification methods on the structures and free radical scavenging abilities of Laminaria japonica polysaccharides, carboxymethylation, sulfation and phosphorylation methods were used to modify chemically Laminaria japonica polysaccharides. Ultraviolet spectroscopy, Fourier transform infrared spectroscopy, Congo red experiment, periodate oxidation and free radical scavenging ability experiments were used to compare the differences in the structure and DPPH•, •OH and O2-• scavenging abilities of Laminaria japonica polysaccharides before and after modification. The results showed that -OH was transformed into -COO, O-S and P-OH, respectively, indicating that carboxymethylation, sulfation and phosphorylation of Laminaria japonica polysaccharides were successful in the modification of Laminaria japonica polysaccharides. Compared with the polysaccharide before modification, the threestrand helix structure disappeared after modification. There were significant differences in the bond types of glycosidic bonds before and after modification: the glycosidic bond types of the Laminaria japonica polysaccharides and the phosphorylated Laminaria japonica polysaccharides were (1→6), (1→2, 1→4), (1→3), with their molar ratios being 0.04:0.05:0.91 and 0.03:0.05:0.92, respectively. The glycosidic bond types of carboxymethylated Laminaria japonica polysaccharide and sulfated Laminaria japonica polysaccharide were (1→2, 1→4) and (1→3), with their molar ratios being 0.02:0.98 and 0.10:0.90, respectively. The scavenging rates of carboxymethylated Laminaria japonica polysaccharide and phosphorylated Laminaria japonica polysaccharide against DPPH•, •OH and O2-• increased by 7.38%, 12.17% and 0.78%, and 9.12%, 40.22% and 14.52%, respectively. The scavenging rates of sulfated Laminaria japonica polysaccharides against DPPH• and O2-• increased by 24.48% and 5.16%, respectively, whilst the scavenging ability against •OH was weakened, with the scavenging rate being reduced by 34.82%. The analysis of comprehensive scores revealed that the half-maximal inhibitory concentrations (IC50 values) of the carboxymethylated, sulfated and phosphorylated Laminaria japonica polysaccharides were 2.53, 4.03 and 1.66 mg/mL, respectively, indicating that phosphorylation modification was superior to carboxymethylation modification and sulfation modification in improving the free radical scavenging ability of Laminaria japonica polysaccharide.