Objective · To evaluate the clinical value of the electromagnetic navigation system for precutaneous transthoracic needle biopsy. Methods · A prospective randomized controlled trial was carried out. One hundred and thirteen patients who needed to have lung nodule biopsy were divided into two groups according to the random number table: the auxiliary puncture group (n=57) adopting the electromagnetic navigation system for precutaneous transthoracic needle biopsy, and the conventional operation group (n=56) adopting the traditional CT-guided transthoracic needle biopsy. The operation process of the two groups was completed by junior doctors under the supervision and guidance of senior doctors. The time of puncture, the number of CT scan, and postoperative complications were observed and compared between the two groups. Results · There was no significant difference in operation time between the auxiliary group and the conventional group [(26.7±8.0) min vs (25.0±7.8) min, P=0.261)]. There was no significant difference in the number of CT scan between the two groups (4.9±2.7 vs 5.1±2.7, P=0.810). There was no significant difference in the incidence rate of pneumothorax (15.8% vs 19.6%, P=0.592) and bleeding (17.5% vs 14.3%, P=0.636) between the two groups. Conclusion · The domestic electromagnetic navigation system for precutaneous transthoracic needle biopsy can safely and effectively assist clinicians to complete lung biopsy.