To investigate mechanism of migration and invasion effected by carboxyl terminal activating region 3 (CTAR₃) of Epstein-Barr virus encoded latent membrane protein 1(LMP1) in nasopharyngeal carcinoma stem cell SP18 cells, the SP18 cell of stable expressed LMP1 and deletion mutant type LMP1 (LMP1^△232-351) were established (SP18-LMP1 and SP18-LMP1^△252-351). The effect of LMP1-CTAR₃ deletion mutant for cellular proliferation, migration and invasion were observed in SP18 cells. The differential expression genes between SP18-LMP1 and SP18-LMP1^△252-351 cells were analyzed by cDNA chips, and the expression levels of partial identified genes were verified by fluorescent Real-time quantitative RT-PCR. The relation of differential expression genes were analyzed by bioinformatics. The results showed: (1) The ability of LMP1^△232-351 promoting SP18 cell proliferation, migration and invasion was obviously decreased to compare with wild type LMP1(n=3, P < 0.05). (2) 18 genes, 13 up- and 5 down-regulated ones, of LMP1-CTAR₃ mediated regulation with migration and invasion were identified from in SP18 cell lines. The differential expression of partial identified genes was similar with cDNA chips separated ones and confirmed by fluorescent Real-time quantitative RT-PCR. (3) 13 differential expression genes can be cross-talk, and among FN1, MMP14, ITGA2, THBS1, IL1B and IL6 genes were frequently correlation. These results suggested that LMP1-CTAR₃ probably regulates the expression of FN1, MMP14, ITGA2, THBS1, IL1B and IL6 genes to induce and promote migration and invasion of nasopharyngeal carcinoma stem cell SP18 cell.