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This paper introduces KG-FLoc, a knowledge graph-enhanced framework for secondary circuit fault localization in intelligent substations. The proposed KG-FLoc innovatively formalizes secondary components (e.g., circuit breakers, disconnectors) as graph nodes and their multi-dimensional relationships (e.g., electrical connections, control logic) as edges, constructing the first comprehensive knowledge graph (KG) to structurally and operationally model secondary circuits. By reframing fault localization as a knowledge graph link prediction task, KG-FLoc identifies missing or abnormal connections (edges) as fault indicators. To address dynamic topologies and sparse fault samples, KG-FLoc integrates two core innovations: (1) a relation-aware gated unit (RGU) that dynamically regulates information flow through adaptive gating mechanisms, and (2) a hierarchical graph isomorphism network (GIN) architecture for multi-scale feature extraction. Evaluated on real-world datasets from 110 kV/220 kV substations, KG-FLoc achieves 97.2% accuracy in single-fault scenarios and 93.9% accuracy in triple-fault scenarios, surpassing SVM, RF, MLP, and standard GNN baselines by 12.4–31.6%. Beyond enhancing substation reliability, KG-FLoc establishes a knowledge-aware paradigm for fault diagnosis in industrial systems, enabling precise reasoning over complex interdependencies.