From July 2022 to May 2023， 30 sampling sites were established in the south branch， north branch， and dongtan of Chongming Island of the Yangtze River estuary to investigate the seasonal distribution of Coilia nasus，Coilia mystus and their relationships with environmental factors. Field sampling was conducted seasonally using a large larval fish net （mouth diameter： 1.3 m， mesh size： 0.5 mm） for surface horizontal towing， with each tow lasting 10 minutes at a speed of 2 knots. This study aimed to understand the distribution patterns of these two fish species and their responses to seasonal environmental variations in this estuarine ecosystem. The generalized additive model （GAM） was used to analyze the correlation between the abundance of fish larvae and juveniles and environmental factors. The results showed that spring and summer were the main breeding periods for C. nasus and C. mystus in the Yangtze River estuary. C. nasus larvae and juveniles were mainly distributed in the waters near the south branch and the north branch and the dongtan of Chongming Island， In contrast， C. mystus eggs were distributed in the waters from Changxing Island to Jiuduansha in the south branch and in the waters outside the entrance to the north branch， while larvae and juveniles were predominantly found outside the south branch， the north branch， and the dongtan of Chongming Island. GAM analysis revealed significant seasonal patterns in the utilization of the Yangtze River estuary as spawning and nursery grounds by both species. Summer had a significant positive effect on the abundance of C. nasus larvae and juveniles， while both spring and summer positively influenced the abundance of C. mystus larvae and juveniles， with summer showing significantly higher effects than spring （P<0.01）. Salinity had a significant impact on the abundance of C. nasus （P<0.01）. The suitable salinity for C. nasus larvae and juveniles was 0-6 PSU. The distribution of C. mystus larvae and juveniles was mainly affected by temperature， salinity， and pH （P<0.01）. The suitable temperature was 20-32 ℃， the suitable salinity was 2-16 PSU， the suitable pH was 7.3-8.2 and the suitable dissolved oxygen ranged from 6.0 to 9.0 mg/L. The interactive effects of environmental factors， temperature-salinity and temperature-pH exhibited significant impacts on the abundance of C. nasus larvae and juveniles. Overlapping nursery grounds were observed between the two species， with variations in spatial distribution across different developmental stages. The findings contribute to a better understanding of the ecological dynamics in the Yangtze River estuary and offer guidance for the conservation and management of these two species.