Pediatric liver tumors are one of the most common solid tumors in pediatrics, with differentiation of benign or malignant status and pathological classification critical for clinical treatment. While pathological examination is the gold standard, the invasive biopsy has notable limitations: the highly vascular pediatric liver and fragile tumor tissue raise complication risks such as bleeding; additionally, young children with poor compliance require anesthesia for biopsy, increasing medical costs or psychological trauma. Although many efforts have been made to utilize AI in clinical settings, most researchers have overlooked its importance in pediatric liver tumors. To establish a non-invasive examination procedure, we developed a multi-stage deep learning (DL) framework for automated pediatric liver tumor diagnosis using multi-phase contrast-enhanced CT. Two retrospective and prospective cohorts were enrolled. We established a novel PKCP-MixUp data augmentation method to address data scarcity and class imbalance. We also trained a tumor detection model to extract ROIs, and then set a two-stage diagnosis pipeline with three backbones with ROI-masked images. Our tumor detection model has achieved high performance (mAP=0.871), and the first stage classification model between benign and malignant tumors reached an excellent performance (AUC=0.989). Final diagnosis models also exhibited robustness, including benign subtype classification (AUC=0.915) and malignant subtype classification (AUC=0.979). We also conducted multi-level comparative analyses, such as ablation studies on data and training pipelines, as well as Shapley-Value and CAM interpretability analyses. This framework fills the pediatric-specific DL diagnostic gap, provides actionable insights for CT phase selection and model design, and paves the way for precise, accessible pediatric liver tumor diagnosis.