In gauge/gravity duality, matrix degrees of freedom on the gauge theory side play important roles for the emergent geometry. In this paper, we discuss how the entanglement on the gravity side can be described as the entanglement between matrix degrees of freedom. We consider several classes of quantum states to which our approach can play important roles. When applied to fuzzy sphere, matrix entanglement can be used to define the usual spatial entanglement in two-brane or five-brane world-volume theory nonperturbatively in a regularized setup. Another application is to a small black hole in AdS5×S5 that can evaporate without being attached to a heat bath, for which our approach suggests a gauge theory origin of the Page curve. The confined degrees of freedom in the partially-deconfined states play the important roles.