In this study, eleven representative seaweeds were sampled in raft-mussel-culture area, Gouqi Island during the flourishing period of seaweeds. And biological parameters of seaweeds and amphipods associated with each seaweed species were measured. Results showed that the population characteristics of Gammaridea and Caprellidae attached on different seaweed species were significantly different. Both of the highest population density and the largest body size of Gammaridea appeared on Pachydictyon coriaceum. And the highest population density and the largest body size of Caprellidae appeared on Ganonema farinosum and Grateloupia constricata, respectively. Moreover, seaweed species with relatively lower biomass tended to support higher population density of Gammaridea and Caprellidae and smaller size of Caprellidae, but had no significant effect on size of Gammaridea. Furthermore, seaweed with higher surface area to biomass ratio tended to support higher density and larger body size of Gammaridea, but had no significant effect on density or body size of Caprellidae. In a word, our investigation indicated that seaweeds community paly different functional roles in structuring seaweed-associated amphipods population characteristics in mussel raft culture area, which were determined by the diverse seaweed biological traits.