Background Atrial fibrillation (AF) adversely affects surgical outcomes of cardiac valve surgery. Surgical ablation is an effective way to treat valvular AF. The aim of this study was to evaluate the late outcome of surgical radiofrequency ablation and explore the risk factors of AF recurrence in Chinese patients undergoing cardiac valve surgery. Methods Three hundred ninety six consecutive patients with persistent valvular AF were enrolled in this study. They underwent concomitant modified Maze IV and were completed follow-ups. Cox survival regression model was used to screen independent risk factors for predicting late recurrence of AF. Results During the follow-up period of 28 (6 ~ 61) months, AF recurred in 151 patients (38.1%). In multivariate survival regression, factors predictive of AF late recurrence were AF duration, pre-operative serum B-type natriuretic peptide (BNP), pre-operative heart rate and left atrial diameter (LAD), post-operative atrial tachyarrhythmias and AF at discharge. According to receiver operating characteristic curve analysis, the best cutoff values for AF duration, BNP, heart rate and LAD were 66.5 months, 251 pg/ml, 82 beats/min and 67.9 mm, respectively. Conclusions Longer AF duration, larger LAD, higher BNP level and lower heart rate indicated a poor late outcome of surgical radiofrequency ablation in persistent AF patients undergoing cardiac valve surgery. Therefore, indication to radiofrequency ablation should be carefully considered in these patients. Electronic supplementary material The online version of this article (doi:10.1186/s13019-017-0627-z) contains supplementary material, which is available to authorized users.