Aiming at the limitations of traditional medical decision system in processing large-scale heterogeneous medical data and realizing highly personalized recommendation, this paper introduces a personalized medical decision algorithm utilizing graph neural network (GNN). This research innovatively integrates graph neural network technology into the medical and health field, aiming to build a high-precision representation model of patient health status by mining the complex association between patients' clinical characteristics, genetic information, living habits. In this study, medical data is preprocessed to transform it into a graph structure, where nodes represent different data entities (such as patients, diseases, genes, etc.) and edges represent interactions or relationships between entities. The core of the algorithm is to design a novel multi-scale fusion mechanism, combining the historical medical records, physiological indicators and genetic characteristics of patients, to dynamically adjust the attention allocation strategy of the graph neural network, so as to achieve highly customized analysis of individual cases. In the experimental part, this study selected several publicly available medical data sets for validation, and the results showed that compared with traditional machine learning methods and a single graph neural network model, the proposed personalized medical decision algorithm showed significantly superior performance in terms of disease prediction accuracy, treatment effect evaluation and patient risk stratification.