Accurate localization of multi-focal ground-glass opacities (GGOs) is crucial for successful video-assisted thoracoscopic surgery (VATS). Electromagnetic navigation bronchoscopy (ENB) provides a minimally invasive and dependable approach for precise localization. This study assessed the accuracy and safety of ENB-guided localization in cases involving multi-focal GGOs. This retrospective study presents a single-center investigation into ENB-guided localization, utilizing methylene blue, for multi-focal GGOs assisting VATS. Clinical, surgical, and pathological data were collected from patients who underwent ENB-guided localization between 23 December 2019 and 31 August 2022. The study examined 57 patients with multi-focal GGOs who underwent ENB-guided localization and VATS. A total of 150 GGOs were treated, with ENB-guided localization taking a median time of 65min. Following localization, all patients proceeded to VATS, with a median duration of 170min. The median lesion size measured 7.8mm, with a 5-mm distance between GGO and pleura or fissure. When the distance between GGO and pleura/fissure exceeded 1cm, an additional location point was introduced below the pleura or fissure based on GGO location. No complications related to localization were observed. The overall malignancy rate stood at 66%. Location precision was confirmed by measuring the marker-to-GGO lesion distance, resulting in a 94% (141/150) accuracy rate for GGO localization. ENB-guided methylene blue injection is a safe and precise method to treat multi-focal GGOs, potentially minimizing operation time and simplifying lesion detection.