Diarrhea-predominant irritable bowel syndrome (IBS-D) is a common chronic non-organic gastrointestinal disorder often associated with low-grade intestinal inflammation that disrupts gut function. However, current therapies remain inadequate for achieving sustained symptom relief. In this study, chlorogenic acid-derived carbon nanoparticles (CHA CNs), synthesized via a hydrothermal method, were further encapsulated within ssDNA aptamer modified chitosan (Apt-CS) to yield a multifunctional nanomedicine (Apt-CS@CHA CNs) with anti-inflammatory, ROS-scavenging, and microbiota-regulating properties. In vitro, Apt-CS@CHA CNs exhibited remarkable ROS-scavenging ability and inhibited inflammatory factor expression. In IBS-D mouse model, the formulation demonstrated enhanced colon-targeted delivery, prolonged retention in inflamed tissue, and effective therapeutic outcomes-including reduced inflammation, restored intestinal barrier function, and rebalanced gut microbiota. These findings suggest that Apt-CS@CHA CNs represent a promising platform for targeted therapy in IBS-D.