Objective To explore the emergence agitation resulting from postoperative indwelling urethral catheters in patients of thoracic surgery. Methods In this prospective cohort study, we recruited 140 patients who were scheduled for thoracic surgery under general anesthesia in West China Hospital from January through April 2014. These patients were divided into two groups including a control group and a trial group with 70 patients in each group. The patients in the control group had indwelled urethral catheter routinely. The catheter removed after the surgery at operation room in the trial group. Intraoperative urinary volume, emergence agitation (EA) occurrence, postoperative urinary retention, and urethral irritation were recorded. Results There was no statistical difference in postoperative urinary retention rate between the control group and the trial group (1.43% vs. 2.86%, P=0.230). However, the urethral irritation rate in the control group was significantly higher than that in the trial group (12.86% vs. 0.00%, P=0.012) . And there was a statistical difference in adverse event rate (2.86% vs. 0.00%, P=0.039) between the two groups. There was a significantly higher incidence of urethral irritation in male patients (20.51%, 8/39) than female patients (3.23%, 1/31, P=0.033).The rate of EA in the control group was significantly higher than that in the trial group (28.57% vs. 12.86%, P=0.010). There was a significantly higher EA rate in the patients who had urethral irritation by postoperative indwelling catheters compared with those without indwelling catheters (45.00% vs. 12.86%, P=0.043). Conclusion This study suggests that postoperative EA is a result from urethral irritation than local pain, and the EA rate can be decreased by removal of catheter before anaesthetic recovery.