The rapid growth of scientific literature demands efficient methods to organize and synthesize research findings. Existing taxonomy construction methods, leveraging unsupervised clustering or direct prompting of large language models (LLMs), often lack coherence and granularity. We propose a novel context-aware hierarchical taxonomy generation framework that integrates LLM-guided multi-aspect encoding with dynamic clustering. Our method leverages LLMs to identify key aspects of each paper (e.g., methodology, dataset, evaluation) and generates aspect-specific paper summaries, which are then encoded and clustered along each aspect to form a coherent hierarchy. In addition, we introduce a new evaluation benchmark of 156 expert-crafted taxonomies encompassing 11.6k papers, providing the first naturally annotated dataset for this task. Experimental results demonstrate that our method significantly outperforms prior approaches, achieving state-of-the-art performance in taxonomy coherence, granularity, and interpretability.