Objective To evaluate the diagnostic yield and safety of two biopsy methods, electromagnetic navigational bronchoscopy (ENB) and transthoracic needle biopsy (TTNB), in peripheral pulmonary lesions. To select a low-risk and high-benefit biopsy method based on the clinical characteristics of the lesions and patients. Methods A retrospective analysis was conducted on inpatients who underwent ENB and/or TTNB for peripheral pulmonary lesions in Huadong Hospital Affiliated to Fudan University. Propensity score matching was used to compare the diagnostic yield and safety of the two biopsy methods. Results A total of 126 patients were included in the ENB group, and 104 patients in the TTNB group. After propensity score matching, 83 matched pairs were obtained. The TTNB group exhibited a significantly higher diagnostic yield compared with the ENB group (90.4% vs. 48.2%, P<0.001), but it was also associated with a higher incidence of pneumothorax (1.2% vs. 21.7%, P<0.001). In the ENB group, the diagnostic efficacy was correlated with lesion diameter (P<0.001, OR=0.183, 95%CI 0.071 - 0.470), but there was no statistically significant difference in the diagnostic yield among different lung segments (P>0.05). In the TTNB group, lesion characteristics did not significantly affect the diagnostic yield, but a lesion diameter ≤30 mm (P=0.019, OR=5.359, 95%CI 1.320 - 21.753) and a distance from the pleura ≥20mm (P=0.030, OR=6.399, 95%CI 1.192 - 34.360) increased the risk of pneumothorax. When stratified based on lesion and patient blood characteristics, no significant difference was found in the diagnostic yield between the two groups for characteristics such as left upper lobe (P=0.195), right middle lobe (P=0.333), solid with cavity (P=0.567), or abnormal serum white blood cell count (P=0.077). However, the incidence of pneumothorax in the TTNB group was higher than that in the ENB group. Conclusions The diagnostic yield of ENB is affected by the size of the lesion, while the incidence of pneumothorax in TTNB is influenced by both lesion size and distance from the pleura. In cases with lesions located in the left upper lobe, right middle lobe, solid with cavity, or with abnormal serum white blood cell count, selecting ENB for biopsy is considered preferable to TTNB.