The egg-laying rate is an important indicator of egg production of laying ducks. Egg production directly impacts the economic benefits of the duck industry. In order to obtain better insight into the molecular mechanisms associated with the process of egg production, comparative transcriptomic analysis of the ovaries of Jinding ducks with high and low egg production was performed using the Illumina HiSeq 2500 system. A total of 843 differentially expressed genes (DEGs) was identified, 367 that were down-regulated and 476 that were up-regulated in high egg production (HEP) ovaries, as compared with low egg production (LEP) ovaries. Some genes, such as MC5R, APOD, ORAI1, and DYRK4, were more active in HEP ovaries, indicating that these genes may play important roles in regulation of egg production. Among these 843 DEGs, 685 were assigned to gene ontology (GO) categories. Of these, 25 genes were related to reproduction, and 30 were related to the reproductive process, including some associated with ovarian follicle development, circadian regulation of gene expression, circadian rhythm, and estrogen receptor binding. Furthermore, some important functional pathways were revealed, such as the steroid biosynthesis pathway, the endocrine and other factor-regulated calcium reabsorption pathways, circadian rhythm, the neuroactive ligand-receptor interaction pathway, fatty acid biosynthesis, and the calcium-signaling pathway, which appear to be much more active in the HEP group, as compared to those of the LEP group. The results of this study provide very useful information that may contribute to future functional studies of genes involved in bird reproduction.