Objective To investigate the safety of radiofrequency ablation for reducing inflammatory cytokines and the left atrial diameter in patients with atrial fibrillation (AF). Methods A total of 200 patients with AF who were admitted to our hospital from December 2015 to April 2017 were included in this prospective analysis. Fifty patients were treated with conventional AF medication alone (AF medication group) and 50 patients received radiofrequency ablation (RFA) on the basis of conventional medication (RFA group). Results After treatment, the AF medication group showed significantly higher levels of high-sensitivity C-reactive protein, interleukin-6, carboxyterminal propeptide of type-I procollagen, procollagen type III N-terminal propeptide, and matrix metallopeptidase-9 than the RFA group. The AF medication group had a significantly lower activated partial thromboplastin time, thrombin time, and prothrombin time than the RFA group. A significantly smaller left atrial diameter was observed in both groups after treatment, but this decrease was more pronounced in the RFA group than in the AF medication group. The total treatment efficacy rate was significantly lower in the AF medication group than in the RFA group. Conclusions For patients with AF, RFA leads to a lower incidence of inflammatory responses, faster recovery of cardiac function, and good safety.