Coilia nasus is an important migration type species in the Yangtze River, and has now become a national key protection resource. In order to investigate the temporal-spatial distribution of Coilia nasus in the Yangtze River estuary, according to the survey data of the fishery resources investigation in Shanghai Yangtze estuarine nature during year 2012-2014, we analyzed the relationship between relative abundance index (RAI) and water depth, water temperature and salinity in the Yangtze River estuary, meanwhile established habitat Suitability Index (HSI) model. The results show that the RAI of spring and winter was higher, and was mainly distributed near southern branch of the Yangtze estuary. The population of Coilia nasus habitat in the pelagic area where water depth below 10 m, salinity range of 0-1.0. There is a gentle change between Tem and Suitability Index (SI) in spring, and the maximum value of SI in summer and autumn appeared at 22.5℃ and 28.5℃ respectively, in winter the population had concentrated distribution with the temperature about 15℃.Regression analysis shows that using the geometric mean method can reflect the temporal-spatial distribution in the Yangtze River estuary better. We analyzed that the influence of different seasons and different environmental factors on the distribution of Coilia nasus,based on HSI model we discussed the temporal-spatial distribution of Coilia nasus,also evaluated the selection of HSI model.Aimed at providing some references for protecting Coilia nasus population and then rehabilitating the Yangtze estuary ecosystem.