During June, August and October 2006, there were three multi-disciplinary surveys carried out in the Changjiang River estuary and its adjacent waters (122°00′–125°00′E, 27°50′–34°00′N) by R/V Beidou to study the species composition and abundance of ichthyoplankton (including fish eggs, larvae and juveniles), the spatial distribution of fish spawning ground and their relationship with habitat factors. There were 29, 29 and 25 grid stations sampled in the three cruises, respectively. The ichthyoplankton samples were collected by horizontally towing with a macro-plankton net (mouth diameter 80 cm, length 270 cm, mesh size 0.50 mm) at the sea surface, and the towing speed was 3.0 n mile/h at each sampling station. The towing lasted for 10 min. After hauling for each station, habitat factors including temperature and salinity were measured by Sea Bird-25 CTD. Samples were preserved in 5% formaldehyde solution immediately after sampling for analysis in laboratory. Since the trawl speed could not be accurately evaluated due to the effects of ocean currents and wind-induced wave, the amount of ichthyoplankton was evaluated by actual number of the sampling haul in each station. Ichthyoplankton collected were divided into three categories: dominant species, important species and main species by the index of relative importance ( IRI). There are 71 species (including 1200 fish eggs and 2575 fish larvae and juveniles) collected during 3 cruises and 59 species have been correctly identified to species level, which belongs to 50 genera, 37 families and 9 orders; while 5 species can only be identified to genera level, 1 species only identified to family level and 6 species identified to order level. These 59 species identified to species level and 5 species identified to genera level are divided into three ecological patterns, i.e., brackish water species, neritic water species and coastal water species. Warm water species have 34 species in those 59 species identified to species level, accounting for 57.63%, warm temperature species have 25 species, accounting for 42.37%. According to the analysis of IRI, the dominant species are Engraulis japonicus (in June and August, that is important species in October), Scomber japonicus (in August), and Johnius grypotus (in October) during the survey; important species are Cynoglossus joyneri (in June and August), Trichiurus lepturus (in June, August and October), Gonorhynchus abbreviatus (in August), Stolephorus commersonii (in October), Saurida undosquamis (in October) and Saurida elongate (in October), and main species have 12 species in June, 9 species in August and 10 species in October, respectively. The amount of fish eggs and larvae of the dominant species, important species and main species (28 species) are 97.50% and 97.13% of the total amount of fish eggs and larvae, respectively, which are the important composition of fish eggs and larvae in the Changjiang River estuary and its adjacent waters. In June and August of 2006, if compared with that in corresponding months in 1986, there are great changes in the habitat factors especially for temperature and salinity in the investigating areas: high salinity water from off-shelf is much closer to the coastal areas which results in the dramatic increase of sea surface salinity during all three surveys. Sea surface temperature, on the other hand, decreases distinctively in June, but significantly increases in August. The run-off of the Changjiang River greatly reduced due to the long-term drought in summer 2006, which is responsible for the great changes of habitat factors in the Changjiang River estuary and its adjacent waters. The habitat of the Changjiang River estuary is greatly changed, which consequently has significant influences on the spawning, breeding and the spatial distribution of spawning ground of neritic water species, such as Sardinella zunasi, Thryssa kammalensis, Thryssa mystax, Setipinna taty and S. commersonii ect, and coastal water species, such as Ilisha elongate and Konosirus punctatus ect.