蛋白质三级结构（英语：Protein tertiary structure）是在生物化学里指蛋白质整体几何形状，亦称为其折叠。蛋白质分子是一连串的胺基酸一条线地接结，基本上假定其会有一可作用其生物功能的三维结构。对蛋白质三级结构的研究称为结构生物学。蛋白质的三级结构是由它的原子坐标定义的。这些坐标可参照或一个蛋白质结构域或整个三级结构。许多三级结构可以折叠形成一个四级结构。

The term protein tertiary structure refers to a protein's geometric shape. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure. A number of tertiary structures may fold into a quaternary structure.