Much evidence shows that omega-3 polyunsaturated fatty acids (n-3PUFAs) protect the heart by reducing heart rate, increasing heart rate variability, decreasing atrial fibrillation, and preventing ventricular fibrillation arrhythmias and sudden cardiac death. However, some researches suggest that n-3PUFAs exert pro-arrhythmic action. The purpose of this review was to summarize the effects of n-3PUFAs on ion channels and anti-arrhythmic mechanism. Acute administration and long-term use of n-3PUFAs have quite different electrophysiological actions, indicating their anti- and pro-arrhythmic actions in different clinical settings.