Radio frequency interference (RFI) significantly hampers the target detection performance of frequency-modulated continuous-wave radar. To address the problem and maintain the target echo signal, this paper proposes a priori assumption on the interference component nature in the radar received signal, as well as a method for interference estimation and mitigation via time–frequency analysis. The solution employs Fourier synchrosqueezed transform to implement the radar’s beat signal transformation from time domain to time–frequency domain, thus converting the interference mitigation to the task of time–frequency distribution image restoration. The solution proposes the use of image processing based on the dual-tree complex wavelet transform and combines it with the spatial domain-based approach, thereby establishing a dual-domain fusion interference filter for time–frequency distribution images. This paper also presents a convolutional neural network model of structurally improved UNet++, which serves as the interference estimator. The proposed solution demonstrated its capability against various forms of RFI through the simulation experiment and showed a superior interference mitigation performance over other CNN model-based approaches.