Background: Changshun green-shell laying hens are unique to Guizhou Province, China, with high egg quality. At this stage, improving egg production performance has become an important breeding task. In recent years, the development of high-throughput sequencing technology provides a fast and exact method for genetic selection. Therefore, this study is based on high-throughput sequencing technology to analyze the differences in the ovarian mRNA transcriptome of low-yield and high-yield Changshun green-shell layer hens, identify critical pathways and candidate genes involved in controlling the egg production rate, and provide basic data for layer breeding.Results: The egg production rates of the low egg production group (LP) and the high egg production group (HP) were 68.00 ± 5.56% and 93.67 ± 7.09%, with extremely significant differences between the groups (p <0.01). Moreover, the egg weight, shell thickness, strength and layer weight of the LP were significantly larger than those of the HP (p <0.05). More than 41 million clean reads per sample were obtained, and more than 90% of the clean reads were mapped to the Gallus gallus genome. Further analysis identified 142 differentially expressed genes (DEGs), and among them, 55 were upregulated and 87 were downregulated in the ovaries. KEGG pathway enrichment analysis identified 9 significantly enriched pathways. Among them, the neuroactive ligand-receptor interaction pathway was the most enriched. GO enrichment analysis indicated that the molecular function GO term: transmembrane receptor protein tyrosine kinase activity, as well as the DEGs identified in this GO term, including PRLR, NRP1, IL15, BANK1, NTRK1, CCK, and HGF may play crucial roles in the regulation of egg production.Conclusions: The above-mentioned differentially expressed genes should be paid attention to in molecular breeding of Changshun green-shell laying hens. Moreover, enrichment analysis suggested that the neuroactive ligand-receptor interaction pathway and receptor protein tyrosine kinases may play crucial roles in the regulation of ovarian function and egg production.