Many changes are taking place in the estuary landscape as a result of urbanization, and the changes also alter the fish community because estuaries function as a critical habitat for fishes. To understand the effect of urbanization on the community structure of estuary fish larvae and juveniles in Gonshytyan Creek when Danhai urbanization program was started in 1997, seasonal occurrence and species composition of estuary fish larvae and juvenile were compared during the period in 1984-1985, 1997-1998, and 2004-2005. Besides, satellite images were used to present the bank transformation from natural to artificial in the three time periods. It was found that the number of fish species (and families) decreased from 111 species (46 families) in 1984-1985 to 94 species (49 families) in 1997-1998 and 40 species (21 families) in 2004-2005. Dramatic loss of fish species after the artificial construction of the urbanization program indicated that the urbanization program might have caused severe damage to the habitat of the fishes in the estuary. Further researches on aquatic environment change are anticipated to clarify the causality.