Community structure of fish in relation to environmental variation was investigated in Nanji Islands National Nature Reserve (NINNR). In order to test this relationship, we delineated 25 survey stations with bottom trawling and measured environmental variables. Samples were taken from November 2013 (autumn), February 2014 (winter), May 2014 (spring) and September 2014 (summer). We found a very strong correlation in space and time between temperature and salinity; abundance and biomass in winter; depth and DO in summer then a strong correlation was found respectively between temperature and biomass; salinity and biomass in winter too and finally a moderate correlation between depth and biomass in spring, (P-value < 0.01) with positive correlation (that the other variable or factor has a tendency to increase). We also found out a negative correlation (P-value < 0.05), respectively between salinity and DO; DO and chlorophyll in summer; temperature and salinity; salinity and DO in spring period (mean that the other variable or factor has a tendency to decrease). A negative correlation observed between temperature, salinity and chlorophyll in winter, spring and autumn period were due by a temperature and salinity window open for species blooms through the movement of the TWC and Jiangzhe coastal current close to shore. By comparing diversity of fish species with environmental factors, the community structure of fish varied significantly as physicochemical parameters changed between different stations for each season. As results and according to the species referencing of environmental factors; species diversity, abundance and evenness vary among different stations, corresponding to significant differences of environmental factors (e.g. physicochemical parameters and chlorophyll-a concentration in different sites). Species richness of microfauna was negatively correlated with salinity levels. Furthermore, they were related to the fish community according to the results. This may be due to the fish community’s adaptability in these different variations of environmental factors, but only tolerant members remaining.