The use of anonymous network has increased dramatically due to the development of network technology and people focus on the network security and privacy. However, anonymous networks are often used for illegal purposes, which has caused a significant increase in illegal transactions in the network. Therefore, it is necessary to investigate methods that can trace illegal transactions in anonymous networks. In this paper, we propose a universal and lightweight Software Defined Network (SDN)-based Meter table Watermarking Traceback scheme (SMWT), which is an active watermarking technology. SMWT uses the Bose-Chaudhuri-Hocquenghem (BCH) code as the encoding method and the flow rate as the carrier for the watermark to effectively trace flows of different communication protocols in various anonymous network environments. It utilises the SDN controller to install flow table entries and meter entries to the SDN switch, which can efficiently change the flow rate and embed the watermark in the flow in a stealthily manner. After the flow passes through the anonymous network, the SDN switch can extract the watermark using the flow rate and identify the two communicating parties. We have conducted experiments on evaluate SMWT in a real anonymous network Tor, including the detection rate and the false positive rate. Compared with other relevant existing schemes, SMWT demonstrates a higher detection rate and a lower false positive rate, as well as high flexibility and stealthiness, low deployment difficulty and controller load.