(1) Background: A typical cardiac cycle consists of a P-wave, a QRS complex, and a T-wave, and these waves are perfectly shown in electrocardiogram signals (ECG). When atrial fibrillation (AF) occurs, P-waves disappear, and F-waves emerge. F-waves contain information on the cause of atrial fibrillation. Therefore it is essential to extract F-waves from the ECG signal. However, F-waves overlap the QRS complex and T-waves in both the time and frequency domain, causing this matter to be a difficult one. (2) Methods: This paper presents an optimized resonance-based signal decomposition method for detecting F-waves in single-lead ECG signals with atrial fibrillation (AF). It represents the ECG signal utilizing morphological component analysis as a linear combination of a finite number of components selected from the high-resonance and low-resonance dictionaries, respectively. The linear combination of components in the low-resonance dictionary reconstructs the oscillatory part (F-wave) of the ECG signal. In contrast, the linear combination of components in the high-resonance dictionary reconstructs the transient components part (QRST wave). The tunable Q-factor wavelet transform generates the high and low resonance dictionaries, with a high Q-factor producing a high resonance dictionary and a low Q-factor producing a low resonance dictionary. The different Q-factor settings affect the dictionaries’ characteristics, hence the F-wave extraction. A genetic algorithm was used to optimize the Q-factor selection to select the optimal Q-factor. (3) Results: The presented method helps reduce RMSE between the extracted and the simulated F-waves compared to average beat subtraction (ABS) and principal component analysis (PCA). According to the amplitude of the F-wave, RMSE is reduced by 0.24–0.32. Moreover, the dominant frequency of F-waves extracted by the presented method is clearer and more resistant to interference. The presented method outperforms the other two methods, ABS and PCA, in F-wave extraction from AF-ECG signals with the ventricular premature heartbeat. (4) Conclusion: The proposed method can potentially improve the accuracy of F-wave extraction for mobile ECG monitoring equipment, especially those with fewer leads.