Background Myopia development is commonly assessed by an increase in axial length, which may lead to high myopia and visual impairment. This study aims to identify potential biomarkers and signaling pathways in the sclera during experimental axial elongation. Methods A myopia guinea pig model was established using male guinea pigs aged 2-3 weeks, which underwent bilateral lens-induced myopization (LIM) (study group) or were left untreated (control group). An integrated analysis of transcriptomic and proteomic was performed to identify differentially expressed genes (DEGs) in the sclera. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to explore the DEGs related signaling pathways. Promising candidate markers were further tested by Western blot analysis. Transmission electron microscopy was used to assess scleral fiber changes in myopic guinea pigs. Results During the study period, axial elongation was significantly greater in the study group (0.59 +/- 0.05 mm vs. 0.47 +/- 0.02 mm; P < 0.001), accompanied by a reduction in the thickness of the retina (121.9 +/- 2.50 mu m vs. 134.6 +/- 0.48 mu m; P < 0.001), choroid (38 +/- 1.0 mu m vs. 50 +/- 0.8 mu m; P < 0.001), and sclera (100.8 +/- 2.78 mu m vs. 155.6 +/- 4.78 mu m; P < 0.001). Integrated transcriptomic and proteomic analyses identified 34 upregulated genes, with significant activation and enrichment of the circadian rhythm pathway. Among the top enriched pathways, key differentially expressed genes included retinoid-related orphan receptors ROR alpha and ROR beta, which are recognized as critical signals modulating the scleral hypoxia response. Western blot analysis confirmed upregulation of ROR alpha, ROR beta, melatonin receptor type 1 (MT1), and HIF-1 alpha in the sclera, while melatonin receptor type 2 (MT2) expression remained unchanged between the groups. Transmission electron microscopy revealed a significantly higher proportion of thin collagen fibers compared to thick fibers in the LIM group (P < 0.05). Conclusions Axial elongation-related remodeling of scleral collagen is closely linked to circadian rhythm and hypoxia pathways, with ROR alpha, ROR beta, melatonin receptors, and HIF-1 alpha identified as potential key regulators. Additionally, scleral fiber size decreases progressively with scleral remodeling in myopia development.