The biological indices of Coilia mystus were studied based on samples collected from May to July 2018 and May and August 2019 in the Yangtze Estuary. The results showed that the average condition factor (K) of female C.mystus was 0.32%, and that of male C.mystus was 0.37%. The average gonadosomatic index(GSI) of female was 18.58%, and that of male was 7.47%. In 2018 and 2019, the egg diameter of C.mystus in the Yangtze Estuary was 0.68 mm and 0.70 mm, respectively. Compared with previous studies, the egg diameter of C.mystus tended to be smaller. The average absolute fecundity of C.mystus in 2018 and 2019 were 11 621 and 6 131, respectively. The difference in absolute fecundity between 2018 and 2019 may be caused by the fecundity difference between different generations. The absolute fecundity and body length relative fecundity of C.mystus were positively correlated with body length, body mass, net body mass and gonad mass, and the body mass relative fecundity (F_W) was significantly correlated with gonad mass and gonadosomatic index. Individual fecundity is most closely related to gonadosomatic index. Stepwise regression showed that the relationship between absolute fertility and biological indices was as follows:F=5 059.50W₁+1 009.00(R²=0.73); F_L=22.77W₁+27.71 (R²=0.76); F_W=2 614.35I_GSI-40.67W₁+412.41(R²=0.60).The spawning fraction of C.mystus in 2018 and 2019 were 0.26 and 0.24 by migratory nucleus method. The difference in sampling time may have caused the annual difference in spawning fraction. The study on the individual fecundity and the spawning fraction of C.mystus in the Yangtze Estuary could provide a key parameter for assessing the spawning stocks biomass of C.mystus in the Yangtze estuary by using the daily egg production method. It provides some reference for the evaluation of restoration effect of C.mystus resources in the Yangtze Estuary in the future.