Objective To identify the core genes of clear cell sarcoma of the kidney (CCSK) based on the Gene Expression Omnibus (GEO) database, and to analyze the immune cell infiltration between tumor and normal tissues, so as to provide a new direction for the diagnosis and treatment of CCSK. Methods Combined analysis of GSE49972 and GSE2712 datasets from GEO database was performed to screen the differentially expressed genes between CCSK and normal embryonic kidney tissues. The Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analyses of the differentially expressed genes were performed and the protein-protein interaction network was constructed to identify the core genes of CCSK. Meanwhile, the immune cell infiltration of CCSK and normal embryonic kidney tissues was analyzed. Results A total of 740 differentially expressed genes were screened out, and the GO function analysis showed that these genes were enriched in the extracellular structure organization, collagen-containing extracellular matrix, cell adhesion molecule binding and so on. The KEGG signaling pathway analysis showed that the major signaling pathways involved in differentially expressed genes mainly included in phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling pathway, trancriptional misregulation in cancer, focal adhesion, calcium signaling pathway and proteoglycans in cancer. The protein-protein interaction network analysis showed that claudin family and cadherin family had large weighted values in the core modules. The immunity cell infiltration analysis showed that the infiltration of most immune cells was low in CCSK tissues, but the infiltration of CD4 T cells was relatively high. Conclusion Claudin and cadherin pathways and core genes play an important role in CCSK and can be potential therapeutic targets. The combination of immune checkpoints and specific kinase inhibitors may improve the immunotherapeutic effect of CCSK.