Three-dimensional (3D) memory devices with 3D phase-change memory (PCM) and methods for forming and operating the 3D memory devices are disclosed. In an example, a 3D memory device includes a first semiconductor structure including an array of NAND memory cells, and a first bonding layer including first bonding contacts. The 3D memory device also further includes a second semiconductor structure including a second bonding layer including second bonding contacts, a semiconductor layer and a peripheral circuit and an array of PCM cells between the second bonding layer and the semiconductor layer. The 3D memory device further includes a bonding interface between the first and second bonding layers. The first bonding contacts are in contact with the second bonding contacts at the bonding interface.