Due to the development of digital radio frequency memory (DRFM), active jamming against the main lobe of the radar has become mainstream in electronic warfare. The jamming infiltrates the radar receiver via the main lobe, covering up the target echo information. This greatly affects the detection, tracking, and localization of targets by radar. In this study, we consider jamming suppression based on the independence of RF features. First, two stacked sparse auto-encoders (SSAEs) are built to extract the RF characteristics and signal features carried out by the actual radar signal for subsequent jamming suppression. This method can effectively separate RF features from signal features, making the extracted RF features more efficient and accurate. Then, an SSAE-based jamming suppression auto-encoder (JSAE) is proposed; the mixed signal, including the radar signal, jamming signal, and noise, is input to JSAE for dimensionality reduction. Therefore, the radar signal and RF features, extracted by the two SSAEs in the previous step, are used to constrain the features of the reduced mixed signal. Moreover, we integrate the feature level and signal level to jointly achieve jamming suppression. The original radar signal is used to assist the radar signal reconstructed by the decoder. By first filtering out interference-related features and then reconstructing the signal, we can achieve better jamming suppression performance. Finally, the effectiveness of the proposed method is verified by simulating the actual collected data.