The emergence of radio frequency machine learning has significantly propelled the application of deep learning (DL) methods in automatic modulation classification (AMC). However, under non-cooperative scenarios, the performance of DL-based AMC suffers severe performance degradation due to scarce labeled samples and noise interference. To enhance noise robustness in few-shot AMC, this paper proposes a complex-domain autoencoder-based method where a complex-valued noise reduction network (CNRN) is embedded into the AMC framework, jointly extracting complex-valued and temporal features from noisy signals to achieve signal–noise separation. Our framework executes four sequential operations: high-signal-to-noise-ratio (high-SNR) samples are first isolated from limited raw data via unsupervised classification; rotation and cyclic time-shifting operations then augment the sample space; the CNRN is subsequently trained on augmented data; and final AMC classification is implemented through DL-based classifiers. Experimental validation on RML 2016.10a dataset demonstrates: (1) for −20 dB signals, denoising achieves 20.18 dB SNR improvement with 87.74% mean squared error reduction; (2) across the −20 dB to 18 dB range, denoised signals exhibit accuracy improvements of 21.57% under DL-based classifiers. Physical validation further confirms that the proposed method exhibits enhanced noise robustness, demonstrating its practical utility in real-world scenarios.