To address the physiological artifacts commonly encountered in EEG-based emotion recognition, this paper proposes FDC-Net, a novel framework that integrates denoising and emotion recognition processes. Unlike existing independent approaches to denoising and emotion recognition, FDC-Net tightly links the two processes through a joint optimization strategy utilizing bidirectional gradient propagation and a gated attention mechanism. Specifically, it integrates a frequency-adaptive transformer that utilizes learnable frequency-band position encoding to enhance efficiency. Experiments are conducted using two representative EEG emotion datasets, DEAP and DREAMER, demonstrating improved denoising and emotion recognition performance compared to existing state-of-the-art methods. FDC-Net achieved correlation coefficients (CCs) of up to 96.30% on the DEAP dataset and up to 90.31% on the DREAMER dataset. The emotion recognition accuracies were 82.3% + 7.1% on DEAP and 88.1% + 0.8% on DREAMER.