Objective To investigate the clinical characteristics, diagnostic approach, multidisciplinary diagnosis and treatment model, and anticoagulation strategies of venous thrombotic disease in children, summarize diagnosis and treatment experience, and provide a reference for improving standardized management of this condition. Methods A retrospective analysis was conducted on clinical data of 40 children with venous thrombotic disease managed by the multidisciplinary team (MDT) at Shenzhen Children's Hospital. Data included demographic characteristics, underlying diseases, risk factors, clinical manifestations, diagnostic procedures, anticoagulation regimens, and clinical outcomes. Results Among the 40 children, the most common risk factor was central venous catheter placement (42%), and the most frequent underlying diseases were malignant tumors (30%) and severe infections (25%). Clinical manifestations were diverse and often insidious, frequently masked by primary diseases. All cases were confirmed by imaging examinations. Anticoagulation mainly involved low-molecular-weight heparin and warfarin, with some patients receiving oral anticoagulants. Following MDT management and individualized anticoagulation therapy, the overall recanalization rate was 98%, the incidence of bleeding was 5%, and no major bleeding events occurred. Conclusions Venous thrombotic disease in children commonly occurs secondary to severe underlying conditions and presents with atypical clinical features, requiring increased diagnostic vigilance. A diagnosis and treatment model centered on an MDT, combined with individualized anticoagulation therapy, effectively improves prognosis and represents an effective strategy for managing these complex cases.