To investigate the possible molecular mechanisms of radiofrequency ablation (RFA) for treating atrial fibrillation (AF) and the microRNA (miRNA) target for intervention in the future. We examined the changes in miRNAs regulating the atrial ion-channel proteins across the whole genome. We compared findings from 90 AF patients with those from 90 healthy subjects before RFA and three months after RFA. Twenty-one miRNAs regulating ion-channel proteins were differentially expressed more than ten-fold, and the findings were completely reversed after RFA as compared with the pre-RFA results. The colonial regulating effects of miRNAs regulating the outward K+ current channels such as those for the ultra-rapid delayed rectifier potassium current (Ikur), voltage-dependent delayed rectifier potassium current (Ikr), and delayed rectifier potassium channel current (Iks) were more unanimous and stronger, while this was not the case for miRNAs regulating the L-type Ca2+ current and INa current channels. Generally, miR-1266 levels were increased in the blood but down-regulated in the rheumatic atrial tissue, while a dual luciferase test indicated that SCN5A was the direct target gene of miR-1266. Using RFA to treat AF may have an impact via reversing the changes in miRNAs regulating the ion-channel proteins, especially for outward K+ current channels such as Ikur, Ikr, and Iks, which may play a major role in electrical remodeling in AF. It may be that miR-1266 is an antiarrhythmic miRNA and an AF intervention target in the future (Tab. 2, Fig. 4, Ref. 46).