Coilia nasus, a migratory fish species naturally inhabiting in the middle and lower reaches of the Yangtze River and offshore China, has high culturing potential and economic value. However, significant variation in the gonadal development rate among female individuals leads to inconsistent ovarian maturation times at the population level, so as to prolong reproductive period, and ovarian pre-maturity also limits fish growth rate. Here, we combined genome-wide association analysis (GWAS) and comparative transcriptome analysis to explore the potential associated SNPs and candidate genes associated with population-asynchronous ovarian development in C. nasus. Genotyping of female population was performed by whole-genome re-sequencing, resulting in the identification of 2,120,695 high-quality SNPs. Thirty-nine SNPs were proved to have suggestive association with ovarian development. A significant SNP peak was obtained on LG21 containing 30 suggestive associated SNPs, and cpne5a gene was identified as the causal gene of the peak. Therefore, single-marker association analysis and haplotype association analysis were performed based on cpne5a, and 4 genetic markers (p < 0.05) and 7 haplotypes (r2 > 0.9) significantly associated with the phenotype were obtained. The comparative transcriptome analysis based on the precocious maturing (PM) and normally maturing (NM) individuals screened out 29 and 426 overlapping differentially expressed genes (DEGs) between different body-size individuals in the brain and ovary, respectively. Combining the results of GWAS and transcriptome analysis, we identified genes and pathways related to HPG axis hormone secretion, extracellular matrix, angiogenesis and gap junctions were involved in population-asynchronous ovarian development. The results of the study provide a basis for in-depth understanding of the molecular mechanism of fish ovarian development, and may facilitate the genetic breeding of population-synchronous ovarian development strains of C. nasus in the future.