LLM pre-training efficacy increasingly depends on data composition rather than sheer volume. Yet, optimal mixing is hindered by categorization flaws: human taxonomies suffer from ontological misalignment, and Euclidean clustering fails to address embedding anisotropy. We introduce GEM (Geometric Entropy Mixing), a framework reformulating data curation as a variational problem on the hypersphere augmented with a mixing-balance regularizer. By decoupling the generative prior and optimizing the objective via a provable MM (Minorize-Maximize) algorithm, GEM effectively counteracts the cluster collapse to discover balanced semantic structures invisible to Euclidean heuristics. We employ teacher-student distillation to scale this geometric fidelity to web-scale corpora and introduce the Geometric Influence Score (GIS) for interpretable taxonomy generation. Experiments with 1.1B-parameter models demonstrate that GEM establishes a new state-of-the-art when integrated into mixing strategies like DoReMi and RegMix, improving average downstream accuracy by up to 1.2% and offering a robust coordinate system for predictable data mixing.