Pre-trained deep learning (DL) models are increasingly accessible in public repositories, i.e., model zoos. Given a new prediction task, finding the best model to fine-tune can be computationally intensive and costly, especially when the number of pre-trained models is large. Selecting the right pre-trained models is crucial, yet complicated by the diversity of models from various model families (like ResNet, Vit, Swin) and the hidden relationships between models and datasets. Existing methods, which utilize basic information from models and datasets to compute scores indicating model performance on target datasets, overlook the intrinsic relationships, limiting their effectiveness in model selection. In this study, we introduce TransferGraph, a novel framework that reformulates model selection as a graph learning problem. TransferGraph constructs a graph using extensive metadata extracted from models and datasets, while capturing their inherent relationships. Through comprehensive experiments across 16 real datasets, both images and texts, we demonstrate TransferGraph's effectiveness in capturing essential model-dataset relationships, yielding up to a 32% improvement in correlation between predicted performance and the actual fine-tuning results compared to the state-of-the-art methods.