Objective To explore the relationship between the expression of nucleoporin 93(NUP93) in hepatocellular carcinoma and the prognosis and clinical features of patients, as well as its influence and mechanism on the biological function of hepatocellular carcinoma. Methods The mRNA expression level of NUP93 in hepatocellular carcinoma and adjacent tissues was analyzed by cancer genome map (TCGA) database, and verified by gene expression synthesis (GEO) database. Bioinformatics method was used to analyze the relationship between the expression of NUP93 and the survival prognosis and clinical characteristics of patients, and the relationship between NUP93 and immune cell infiltration. Transfection was performed using the small interfering siNUP93 and transfection reagents according to the instructions and experimental steps, and the hepatocellular carcinoma cells were divided into a control group (siCtrl) and knockdown groups (siNUP93#1 and siNUP93#2)。The effects of down-regulating NUP93 on the proliferation and invasion and migration of hepatocellular carcinoma cells were detected by CCK8, colony formation, cell scratch and Transwell invasion and migration experiments. Genome enrichment analysis (GSEA) was used to enrich and analyze the signal pathways that NUP93 might participate in, and the influence of down-regulation of NUP93 on the possible regulated signal pathway proteins was verified by western blot experiments. Results The expression levels of NUP93 in liver cancer tissues were significantly increased. The high expression of NUP93 can lead to short survival time and malignant progression of tumor, which is closely related to immune cell infiltration. The experimental results showed that down-regulation of NUP93 inhibited the proliferation, migration and invasion of hepatocellular carcinoma cells, and decreased the levels of p-ERK, MMP2 and MMP9. Conclusion NUP93 may become a new biomarker and therapeutic target of liver cancer