重叠矩阵是量子化学中用于描述量子力学系统中的基底矢量的集合的矩阵。尤其是对于正交基底，重叠矩阵是对角线的。此外，如果基底矢量形成了正交的集合，重叠矩阵就是单位矩阵。重叠矩阵总是n×n，其中n是基底函数的数目。这是一个格拉姆矩阵。

总体上，重叠矩阵是这样定义的：

其中

特别的是，如果集合是标准的（不一定正交），对角线上的元素恒为1，而非对角元素的大小总小于或等于这个值。只有存在类似于柯西不等式的线性相关关系时才会取得等号。此外，这个矩阵的定义是恒正的，也就是它的特征值严格为正。

In chemical bonds, an orbital overlap is the concentration of orbitals on adjacent atoms in the same regions of space. Orbital overlap can lead to bond formation. The importance of orbital overlap was emphasized by Linus Pauling to explain the molecular bond angles observed through experimentation and is the basis for the concept of orbital hybridization. Since s orbitals are spherical (and have no directionality) and p orbitals are oriented 90° to each other, a theory was needed to explain why molecules such as methane (CH₄) had observed bond angles of 109.5°. Pauling proposed that s and p orbitals on the carbon atom can combine to form hybrids (sp in the case of methane) which are directed toward the hydrogen atoms. The carbon hybrid orbitals have greater overlap with the hydrogen orbitals, and can therefore form stronger C–H bonds.