Feature analysis is a fundamental research area in computer graphics; meanwhile, meaningful and part-aware feature bases are always demanding. This paper proposes a framework for conducting feature analysis on a three-dimensional (3D) model by introducing modified Non-negative Matrix Factorization (NMF) model into the graphical feature space and push forward further applications. By analyzing and utilizing the intrinsic ideas behind NMF, we propose conducting the factorization on feature matrices constructed based on descriptors or graphs, which provides a simple but effective way to raise compressed and scale-aware descriptors. In order to enable part-aware model analysis, we modify the NMF model to be sparse and constrained regarding to both bases and encodings, which gives rise to Sparse and Constrained Non-negative Matrix Factorization (SAC-NMF). Subsequently, by adapting the analytical components (including hidden variables, bases, and encodings) to design descriptors, several applications have been easily but effectively realized. The extensive experimental results demonstrate that the proposed framework has many attractive advantages, such as being efficient, extendable, and so forth.