Introduction: Lung cancer is a major health concern worldwide owing to its high incidence and mortality rates. Therefore, identification of new therapeutic targets and strategies for lung cancer is critical for improving patient outcomes. Peptidyl arginine deiminase 4 (PAD4) promotes tumor growth and metastasis by catalyzing the citrullination of histones, making it a potential therapeutic target. Although PAD4 inhibitors have shown potential in the treatment of a variety of tumors, existing PAD4 inhibitors lack sufficient specificity and cause substantial systemic adverse reactions. To overcome these challenges, we developed novel YW403@Fe3O4-oxidized carboxymethyl chitosan (OCMC) magnetic nanoparticles (MNPs) that enabled magnetically targeted drug delivery by binding the PAD4 inhibitor YW403 to a ferric oxide magnetic carrier. Methods: In vitro experiments were conducted using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays, Transwell assays, and flow cytometry to evaluate the activity of the MNPs. In vivo experiments involved magnetic resonance imaging (MRI) assessments and inductively coupled plasma mass spectrometry (ICP-MS) analyses to confirm the tumor targeting and iron metabolism of MNPs. Additionally, immunofluorescence staining was employed to further validate the expression of citrullinated histone H3 (H3cit). Results: The implementation of this approach enhanced the targeting efficiency of PAD4 inhibitors, consequently reducing the required dosage of chemotherapy and potentially facilitating MRI monitoring. In vitro experiments demonstrated that MNPs exhibited superior activity compared to free drugs when subjected to an applied magnetic field, due to increased uptake of MNPs by tumor cells. In vivo experiments revealed that the application of magnetic fields significantly improved the tumor targeting of MNPs without impacting iron metabolism. By suppressing the expression of citrullinated histone (H3cit), MNPs effectively inhibited tumor growth and metastasis. Discussion: These findings provide new research ideas for the development of novel anti-tumor nanomaterials and are expected to yield breakthroughs in the treatment of lung cancer.