The Type III Secretion Systems (T3SSs) play a pivotal role in host-pathogen interactions by mediating the secretion of type III secretion system effectors (T3SEs) into host cells. These T3SEs mimic host cell protein functions, influencing interactions between Gram-negative bacterial pathogens and their hosts. Identifying T3SEs is essential in biomedical research for comprehending bacterial pathogenesis and its implications on human cells. This study presents EDIFIER, a novel multi-channel model designed for accurate T3SE prediction. It incorporates a graph structural channel, utilizing graph convolutional networks (GCN) to capture protein 3D structural features and a sequence channel based on the ProteinBERT pre-trained model to extract the sequence context features of T3SEs. Rigorous benchmarking tests, including ablation studies and comparative analysis, validate that EDIFIER outperforms current state-of-the-art tools in T3SE prediction. To enhance EDIFIER's accessibility to the broader scientific community, we developed a webserver that is publicly accessible at http://edifier.unimelb-biotools.cloud.edu.au/ . We anticipate EDIFIER will contribute to the field by providing reliable T3SE predictions, thereby advancing our understanding of host-pathogen dynamics.