With the rapid expansion of web-based applications and cloud services, malicious JavaScript code continues to pose significant threats to user privacy, system integrity, and enterprise security. But, detecting such threats remains challenging due to sophisticated code obfuscation techniques and JavaScript's inherent language characteristics, particularly its nested closure structures and syntactic flexibility. In this work, we propose DeCoda, a hybrid defense framework that combines large language model (LLM)-based deobfuscation with code graph learning: (1) We first construct a sophisticated prompt-learning pipeline with multi-stage refinement, where the LLM progressively reconstructs the original code structure from obfuscated inputs and then generates normalized Abstract Syntax Tree (AST) representations; (2) In JavaScript ASTs, dynamic typing scatters semantically similar nodes while deeply nested functions fracture scope capturing, introducing structural noise and semantic ambiguity. To address these challenges, we then propose to learn hierarchical code graph representations via a Cluster-wise Graph that synergistically integrates graph transformer network, node clustering, and node-to-cluster attention to simultaneously capture both local node-level semantics and global cluster-induced structural relationships from AST graph. Experimental results demonstrate that our method achieves F1-scores of 94.64% and 97.71% on two benchmark datasets, demonstrating absolute improvements of 10.74% and 13.85% over state-of-the-art baselines. In false-positive control evaluation at fixed FPR levels (0.0001, 0.001, 0.01), our approach delivers 4.82, 5.91, and 2.53 higher TPR respectively compared to the best-performing baseline. These results highlight the effectiveness of LLM-based deobfuscation and underscore the importance of modeling cluster-level relationships in detecting malicious code.