We studied the quantum properties of magnetic plasmon waves in a three-dimensional coupled metamaterial. A Hong-Ou-Mandel dip of two-photon interference with a visibility of 86 ± 6.0% was explicitly observed, when the sample was inserted into one of the two arms of the interferometer. This meant that the quantum interference property survived in such a magnetic plasmon wave-mediated transmission process, thus testifying the magnetic plasmon waves owned a quantum nature. A full quantum model was utilized to describe our experimental results. The results showed that the metamaterials could not only steer the classical light but also the non-classical light and they might have potential application in the future quantum information.