Abstract: Embodiments of this application provide omics data processing method and apparatus based on a graph neural network, a device and a medium, and relate to medical, artificial intelligence, cloud data and other technical fields. The method includes: acquiring first omics data of a target object; extracting, at least two first omics features from the first omics data; determining, a first correlation between different omics features; constructing based on the at least two first omics features and the first correlation, a first graph structure corresponding to the first omics data, the first graph structure comprising at least two nodes and at least one connecting edge; obtaining, a node feature of each node in the first graph structure through a first graph neural network based on the first graph structure; and performing medical analysis on the target object based on the node feature.