Abstract: In order to clarify the effects of seawater and freshwater on the ovary development of Coilia nasus, we analyzed their differences by using non-targeted metabolomics, and compared with database of KEGG directly to find out the corresponding metabolic pathways, then analyzed its causes. The results show that a total of 47 metabolites had significant difference between the two groups (P<0.05, FC>1, VIP>1). Compared with the seawater group, the most significant differences in the expression were carbocyclic thromboxane A2, Galactosylceramide, and their differences were 10.40 and 2.78 times, respectively. The cortisol in the ovarian tissue of the freshwater group increased by 1.61 times. According to the analysis on KEGG metabolic pathways of 47 different metabolites, the biosynthesis of aminoacyl-tRNA and pyridine metabolic pathways changed in the seawater and freshwater environments significantly (P<0.05). The biosynthesis pathway of cortisol, aminoyl-tRNA, pyrimidine metabolism pathway and sphingo-lipid metabolism pathway may be related to the ovarian development during the reproductive migration of C. nasus.