This study was purposed to explore the effect of bone marrow derived mesenchymal stem cells (MSCs) on the expression of CD69 on cytokine-induced killer (CIK)/natural killer (NK) cells derived from cord blood and on the quantity ratio of CD4+CD25+ T regulatory cells in CIK/NK cell culture system using Transwell non-contact cell culture system. The experiments were divided into two groups: Transwell non-contact culture and mixture culture. The ratio of MSC to CIK/ NK cells was 1:20, 1:50 and 1:100. In mixture culture groups, MSC and CIK/NK cells were co-cultured by together contact as the same ratio of Transwell non-contact culture groups. The expression of CD69 on CIK/NK cells, as well as the quantity ratio of CD4+CD25+ T regulatory cells in CIK/NK cell culture were evaluated by flow cytometry. The results showed that the expression of CD69 on CIK/NK cells in experimental groups were significantly lower than that in control group (p<0.001). As to Transwell groups, CD69 expression on the CIK/NK cells at 1:20 ratio of MSC and CIK/NK was significantly lower than that at 1:50 and 1:100 ratio. There were no differences in the expression of CD69 on CIK cells in mixture groups with various MSC ratios, whereas the expression of CD69 on NK cells at 1:20 ratio was significantly lower than that at 1:50 and 1:100. The quantity ratio of CD4+CD25+ cells in CIK/NK cell culture system of experimental groups with MSC co-culture was significantly higher than that in control. As to Transwell groups, the ratio of CD4+CD25+ cells in CIK/NK cell culture system at 1:20 and 1:50 was significantly higher than that at 1:100. The quantity ratio of CD4+CD25+ cells in CIK/NK cell culture system showed significant differences in various mixture groups. As to 1:20 ratio the amount of CD4+CD25+ cells in CIK/NK cell culture system of mixture groups was significantly higher than that in Transwell groups, while there were no differences of the quantity ratio of CD4+CD25+ cells in CIK/NK cell culture at 1:50 and 1:100. It is concluded that either by non-contact Transwell or mixed co-culture, the MSC can suppress the activation of allogeneic CB-CIK/NK cells, which maybe relate to up-regulating the ratio of CD4+CD25+ T regulatory cells in CIK/NK cell culture system in dose-dependent manner.