Objective Wool is a high-grade raw textile material, and the physical properties of wool are directly related to the quality of the wool. The present study was to search for the genes affecting wool traits and to explore the complex molecular mechanism affecting wool traits.Methods This study selected 3 Suffolk sheep and 3 small-tailed Han sheep and took samples of their back skin tissue using RNA sequencing (RNA-seq) and proteome sequencing analysis of genes, proteins, and related signalling pathways that cause differences in wool traits.Results RNA-seq showed that after sequencing, 230 406 674 raw data points and 222 049 370 clean data points were obtained, of which the percentage of Q20 bases was over 99.9%, and the percentage of Q30 bases was over 98%. With a fold change (FC)≥1.4 or FC≤0.714 and P<0.05 as the standard, 1 213 differentially expressed genes (DEGs) were screened out, among which there were 644 upregulated genes and 569 downregulated genes in Suffolk sheep in comparison with small-tailed Han sheep. The gene ontology (GO) enrichment found that intermediate filament, calcium ion binding, and keratin filament were significantly enriched, indicating that they might be related to wool traits. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment found that the signalling pathway affecting wool traits might be the ECM-receptor interaction. Proteome sequencing showed that with FC≥1.4 or FC≤0.714 and P<0.05 as the standard, 99 differentially expressed proteins (DEPs) were screened out, among which there were 47 upregulated proteins and 52 downregulated proteins in Suffolk sheep in comparison with small-tailed Han sheep. The GO enrichment found that intermediate filament was significantly enriched, indicating that it might be related to wool traits. The KEGG enrichment found that the signalling pathways affecting wool traits might be the peroxisome proliferator-activated receptor (PPAR) and the ECM-receptor interaction. A combined analysis of RNA-seq and proteome sequencing found that a total of 15 significantly different genes were detected in both RNA-seq and proteome sequencing, of which 13 were positively correlated and 2 were negatively correlated. Intermediate filament was significantly enriched, KRT35, KRT13 and KAP13-1-like genes might be the key candidate genes to affect wool traits. The PPAR signalling pathway was significantly enriched and might be a key candidate pathway to affect wool traits. The FABP4 gene might be a key candidate gene to affect wool traits.Conclusion Among them, KRT35 might affect wool bending and diameter, KRT13 might affect wool differentiation, while KAP13-1-like might affect wool hardness and toughness, FABP4 might affect wool diameter. These results will expand our understanding of the complex molecular mechanisms affecting sheep wool traits and provide a basis for subsequent studies.