Effective and controllable data selection is critical for LLM instruction tuning, especially with massive open-source datasets. Existing approaches primarily rely on instance-level quality scores, or diversity metrics based on embedding clusters or semantic tags. However, constrained by the flatness of embedding spaces or the coarseness of tags, these approaches overlook fine-grained knowledge and its intrinsic hierarchical dependencies, consequently hindering precise data valuation and knowledge-aligned sampling. To address this challenge, we propose Tree-aware Aligned Global Sampling (TAGS), a unified framework that leverages a knowledge tree built from fine-grained tags, thereby enabling joint control of global quality, diversity, and target alignment. Using an LLM-based tagger, we extract atomic knowledge concepts, which are organized into a global tree through bottom-up hierarchical clustering. By grounding data instances onto this tree, a tree-aware metric then quantifies data quality and diversity, facilitating effective sampling. Our controllable sampling strategy maximizes tree-level information gain and enforces leaf-level alignment via KL-divergence for specific domains. Extensive experiments demonstrate that TAGS significantly outperforms state-of-the-art baselines. Notably, it surpasses the full-dataset model by \textbf{+5.84\%} using only \textbf{5\%} of the data, while our aligned sampling strategy further boosts average performance by \textbf{+4.24\%}.