Background: Renal cell carcinoma (RCC) with sarcomatoid differentiation and multiple metastases is highly aggressive RCC with poor prognosis. However, there are not sufficient report on the genetic alterations and tumor immune microenviroment (TIME) of RCC with complex pathological morphology and aggressive behavior.Case presentation: A rare Chinese RCC case with complex pathological morphology and multiple subcutaneous and soft tissue metastases was reported. The clinical manifestations, histomorphology, immunophenotype and follow-up data were collected and analyzed. We performed target region sequencing and immunohistochemistry staining in different morphological regions of the primary tumor and the peritoneal metastasis. Microscopically, this primary tumor was composed of three different histological variations, including ccRCC like region, eosinophilic papillary structure and sarcomatoid differentiation. The peritoneal metastasis partially showed rhabdoid differentiation. IHC staining didn’t display positivity for characteristic markers. IHC for inflammatory cells showed that CD8+T cells and tumor associated neutrophils (TANs) were significantly increased in the sarcomatous areas and peritoneal metastatic tumor. Genomic analysis indicated that VHL mutations were present in all types of pathological regions and peritoneal metastatic tumor. Therefore, the pathological diagnosis of high-grade ccRCC with sarcomatoid differentiation was established. Additionally, we also found SETD2, TP53 and PDGFRA mutations were observed in sarcomatoid tumor area, whereas BRCA2, ATR, CYLD, YAP1 and COL5A3 mutations were specifically detected in peritoneal metastases. These findings are rather striking because some genes e.g., ATR serine/threonine kinase (ATR) and Hippo signaling (YAP1), PI3K-Akt signaling (PDGFRA) and T cell receptor signaling (COL5A3) were previously reported to be very rare in ccRCC patients.Conclusions: Using next-generation sequencing and TIME analysis, multiple low-frequency mutant genes including PDGFRA, ATR, YAP1 and COL5A3 and increased CD8+ T cells and neutrophils were detected in this rare Chinese ccRCC. These findings potentially provide new evidence and molecular markers for accurately assessing the biological behavior of ccRCC.