Currently, Low-Rate Denial of Service (LDoS) attacks are one of the main threats faced by Software-Defined Wireless Sensor Networks (SDWSNs). This type of attack uses a lot of low-rate requests to occupy network resources and hard to detect. An efficient detection method has been proposed for LDoS attacks with the features of small signals. The non-smooth small signals generated by LDoS attacks are analyzed employing the time–frequency analysis method based on Hilbert–Huang Transform (HHT). In this paper, redundant and similar Intrinsic Mode Functions (IMFs) are removed from standard HHT to save computational resources and to eliminate modal mixing. The compressed HHT transformed one-dimensional dataflow features into two-dimensional temporal–spectral features, which are further input into a Convolutional Neural Network (CNN) to detect LDoS attacks. To evaluate the detection performance of the method, various LDoS attacks are simulated in the Network Simulator-3 (NS-3) experimental environment. The experimental results show that the method has 99.8% detection accuracy for complex and diverse LDoS attacks.