Objective To knock out p21 gene in human malignant rhab doid tumor(MRT)cell line G401 by using CRISPR/Cas9 genome engineering technology. Methods The expression of p21 was detected by reverse transcription quantitative PCR (RT-qPCR) and Western blot assay in several MRT cell lines. The guide RNA was designed by targeting the third exon of p21 gene,which encoded its home domains, and then subcloned into lentiCRISPR v2 vector and validated sequencing. The validated plasmids were further used to package and produce the lentivirus in 293T cells, and the G401 cells were infected, then puromycin was used to screen positive cells, and the clusters of G401 monoclonal cells, were obtained by selecting monoclonal cells and culturing under the microscope. The RNA and protein of new clonal cell line were extracted, and RT-qPCR and Western blot assay were applied to confirm whether p21 was successfully knocked out. Results The p21 was highly expressed in MRT tumor cells. The CRISPR/Cas9 lentivirus plasmids, targeted p21 gene were successfully constructed. Compared with negative control group,the expression of p21 was not detected in G401 monoclonal cells, which were successfully screened. Conclusion In view of the difficult transfection of cells such as G401, p21 knockout stable cell line has been successfully constructed by using CRISPR/Cas9 system, which lays the foundation for further study of the mechanism of p21 in MRT tumors .