With the rapid development of the Internet, malware traffic is seriously endangering the security of cyberspace. Convolutional neural networks (CNNs)-based malware traffic classification can automatically learn features from raw traffic, avoiding the inaccuracy of hand-design traffic features. Through the experiments and comparisons of LeNet, AlexNet, VGGNet, and ResNet, it is found that LeNet has good and stable classification ability for malware traffic and normal traffic. Then, a field programmable gate array (FPGA) accelerator for CNNs-based malware traffic classification is designed, which consists of a parameterized hardware accelerator and a fully automatic software framework. By fully exploring the parallelism between CNN layers, parallel computation and pipeline optimization are used in the hardware design to achieve high performance. Simultaneously, runtime reconfigurability is implemented by using a global register list. By encapsulating the underlying driver, a three-layer software framework is provided for users to deploy their pre-trained models. Finally, a typical CNNs-based malware traffic classification model was selected to test and verify the hardware accelerator. The typical application system can classify each traffic image from the test dataset in 18.97 μs with the accuracy of 99.77%, and the throughput of the system is 411.83 Mbps.