Background: The resection of nodules by thoracoscopic surgery is difficult because the nodules may be hard to identify. Currently, preoperative localization of pulmonary nodules is widely used in the clinic, including Computed Tomographic Imaging (CT)-guided transthoracic approach, hook-wire and coil embolization, but these methods increase radiation exposure and cause complications. Methods: In this study, we retrospectively compared electromagnetic navigation bronchoscopy (ENB) guided and CT guided localization of small pulmonary nodules before resection. Results: Total 157 patients underwent the localization procedure successfully, and the nodules were localized by CT guidance in 105 patients and by ENB in 52 patients. The nodule size of magnetic navigation localization was smaller than that of CT-guided localization (P<0.001). Both CT-guided and ENB localization were well tolerated in all patients, without major complications or mortality (P=0.107). In CT-guided localization group, 6 patients failed to be located while none failed in ENB group (P=0.079). The procedure time was 15.15± 3.7 min for CT-guided localization and 21.29± 4.0 min for ENB localization (P<0.001). Conclusions: CT-guided localization is simple and feasible for uncertain pulmonary nodules before surgery. ENB localization could identify small lung nodules with high accuracy and low incidence of complications.