Therapeutic strategies that can target multilevel immunoregulatory pathways in inflammatory bowel disease (IBD) and efficiently target the site of inflammation are expected to greatly enhance the therapeutic efficacy. Here, we have developed a DNA nanorobot-armed bidirectional resistant mesenchymal stem cell (MSC) for IBD treatment, which blocks lymphocyte infiltration at the site of inflammation by bidirectional inhibition of integrin-ligand inter-recognition via resistant aptamer-hands. And this strategy can induce MSC homing for immunomodulation and tissue repair. Herein, in this nanorobot, tetrahedral DNA (TDN) serves as a communication bridge, Integrin α4 and VCAM 1 aptamers are equipped to two vertices of TDN, and the other two cholesterol vertices of TDN are used for immobilization on MSC. In murine colitis models, tail vein-injected resistant MSC preferentially and rapidly accumulated in the inflamed colon and have been more effective in reducing colonic inflammation than pure MSC or aptamers bidirectional inhibitors. The therapeutic strategy proposed in this work has minimal systemic side effects and holds therapeutic promise for a subgroup of IBD patients who do not respond to single anti-inflammatory therapies.