Objective To investigate gene modules associated with atrial fibrillation after percutaneous coronary intervention. Methods The left atrial tissues of 4 patients with atrial fibrillation and 4 patients without atrial fibrillation after percutaneous coronary intervention were collected in Qinghai Provincial Hospital of Cardiovascular and Cerebrovascular Diseases. RNA-Seq was performed to screen out differentially-expressed genes (DEGs). Then gene modules related to atrial fibrillation were constructed using weighted gene co-expression network analysis algorithm. Results Totally 824 DEGs were identified, and several co-expression modules were significantly correlated with atrial fibrillation. Of note, two significant hub genes (RCAN1 and DNAJA4 ) were identified in the gene module associated with the severity of atrial fibrillation. Conclusions Identification of hub genes for atrial fibrillation severity has implications for further understanding the molecular genetic basis of atrial fibrillation.