Populations of Coilia nasus demonstrate asynchronous ovarian development, which severely restricts artificial breeding and large-scale cultivation. In this study, we used a combination of transcriptomic and metabolomic methods to identify the key signaling pathways and genes regulation affecting ovarian development. We identified 565 compounds and generated 47,049 unigenes from ovary tissue. Fifteen metabolites and 830 genes were significantly up-regulated, while 27 metabolites and 642 genes were significantly down-regulated from stage III to stage IV of ovary development. Meanwhile, 31 metabolites and 1,932 genes were significantly up-regulated, and four metabolites and 764 genes were down-regulated from stage IV to stage V. These differentially expressed genes and metabolites were enriched by MetScape. Forty-three and 50 signaling pathways had important functions from stage III-IV and from stage IV-V in the ovary, respectively. Among the above signaling pathways, 39 played important roles from ovarian stage III-V, including "squalene and cholesterol biosynthesis", "steroid hormone biosynthesis", and "arachidonate metabolism and prostaglandin formation" pathways which may thus have key roles in regulating asynchronous development. These results shed new light on our understanding of the mechanisms responsible for population-asynchronous development in fish.