Current audio formats present a fundamental trade-off between file size and functionality: lossless formats like FLAC preserve quality but lack adaptability, while lossy formats reduce size at the cost of fidelity and offer no stem-level access.We introduce the Stem-Native Codec (SNC), a novel audio container format that stores music as independently encoded stems plus a low-energy mastering residual. By exploiting the lower information entropy of separated stems compared to mixed audio, SNC achieves a 38.2% file size reduction versus FLAC (7.76 MB vs. 12.55 MB for a 2:18 test track) while maintaining perceptual transparency (STOI = 0.996). Unlike existing formats, SNC enables context-aware adaptive playback, spatial audio rendering, and user-controlled remixing without requiring additional storage. Our experimental validation demonstrates that the stems-plus residual architecture successfully decouples the conflicting requirements of compression efficiency and feature richness, offering a practical path toward next-generation audio distribution systems.