To understand the status of fish communities in the Qixing Islands Provincial Marine Reserve, China, we carried out bottom trawl surveys during the autumn of 2014 and the spring of 2015. By using niche breadths and their overlaps, non-metric multidimensional scaling and hierarchical cluster dendrograms, we studied the composition of functional groups and niche characteristics of major fish communities. In terms of feeding habits, six functional groups were identified: planktivores, benthivores, piscivores, planktivores/benthivores, benthivores/piscivores and omnivores. Planktivores, benthivores and benthivores/piscivores were the major fish communities in autumn; whereas planktivores, piscivores and omnivores were the dominant fish communities in spring. Shannon-Wiener’s niche breadth index (Bi) and the Pianka’s niche overlap index were used to compare dominant fish species. The niche breadth of dominant fish species ranged from 0.28 and 3.84 in autumn and Harpodon nehereus, Polydactylus sexfilis, Thrissa kammalensis, Odontamblyopus rubicundus, Muraenesox cinereus, Chrysochir aureus and Johnius belengerii had wider niche breadths (Bi>1.0). The niche breadth of dominant fish species ranged from 0.36 and 3.16 in spring and Trichiurus lepturus, Engraulis japonicus, Decapterus maruadsi, Psenopsis anomala, H. nehereus and Pampus argenteus had wider niche breadths (Bi>1.0). The niche overlap of dominant fish species in autumn and spring ranged from 0 to 0.94 and 0 to 0.92, respectively. Based on the square root of the abundance, and using non-metric multidimensional scaling and cluster analysis, fish communities during autumn and spring were divided into four and three groups, respectively. Through the analysis of functional group composition, niche breadth and niche overlap in the Qixing Islands Provincial Marine Reserve, we find improved fish community nutrition structure and spatial structure within the reserve.