In this paper, we propose a simple and low-cost fabrication method for PMMA (Poly (Methyl Methacrylate)) acoustophoretic microfluidic chips using plasma-assisted bonding followed by MEMS (Microelectromechanical Systems) processes. A metal mold for replicating the PMMA polymer was fabricated using MEMS processes, and the microfluidic channel was imprinted on the PMMA polymer using a hot-embossing process. The closed fabricated microfluidic channel was achieved by means of the plasma-assisted bonding between the PMMA channel and the flat PMMA cover. The plasma treatment and hot-embossing conditions for PMMA-PMMA bonding were studied and evaluated. The particle separation test confirmed that the PMMA acoustophoretic microfluidic chips could be used. We expect the Si-based acoustophoretic microfluidic chip to be replaced by the presented polymer chip in such applications as blood or droplet separation.