Rationale: DNA-based nanomedicines have shown significant therapeutic potential for various diseases; however, efficiently utilizing DNA nanomedicines without chemicals or small-molecule drugs is still a major challenge. Methods: In this study, we presented programmed activated DNA hydrogel microcapsules (HAMs) specifically designed for the treatment of inflammatory bowel disease (IBD). It was constructed by encapsulating a DNA hydrogel in sodium alginate microcapsules (AMs) shells. The DNA hydrogel is self-assembled from aptamer-functionalized tetrahedral DNA nanostructures (TDNs) with anti-inflammatory properties and a Y-shaped DNA scaffold in response to ATP. This design provides HAMs with characteristics of precisely targeted release and enhanced local concentrations, thus ensuring better therapeutic outcomes. Results: HAMs exhibited a multistage response to intestinal fluids, a characteristic positive charge at IBD lesions, a high concentration of ATP in the inflammatory microenvironment, and high expression of the membrane protein TLR4 on immune cells, thereby enabling precisely targeted therapy for IBD. Both in vivo and in vitro studies demonstrated that this system possessed precise targeting ability and excellent stability. In a dextran sodium sulfate-induced colitis model, we demonstrated that HAMs effectively alleviate IBD by reducing the production of inflammatory cytokines, restoring the intestinal barrier, and modulating the diversity of the gut microbiota. Furthermore, no significant long-term toxicity of HAMs was detected in the treated mice. Conclusions: This stable, specific, and highly biocompatible system of programmatically activated HAMs overcomes the challenges associated with developing pure DNA nanostructures for therapy and presents a promising approach for IBD treatment.