Objectives To summarize the experiences of CT-guided microcoil localization before video-assisted thoracoscopic surgery (VATS) and to investigate the risk factors associated with pleural marking failure. Methods Totally, 249 consecutive patients with 279 pulmonary nodules who underwent CT-guided microcoil localization prior to VATS were enrolled in this study. According to intraoperative observation, all the nodules were divided into two groups. The clinical characteristics and microcoil localization procedure-related variables of the nodules were analyzed by univariate analysis and multivariate logistic regression analysis to screen the independent factors associated with procedure results. Results Among the 279 nodules, 28 failed to observe the proximal end of the microcoil deployed on visceral pleura during VATS. The logistic regression revealed that needle-pleura angle (<= 30 degrees: OR = 39.022,p = 0.003), pleura-microcoil distance (<= 10 mm: OR = 87.054,p < 0.001; 10 similar to 20 mm: OR = 10.088,p = 0.010), and presence of pleural indentation (OR = 21.623,p < 0.001) were independent risk factors for pleural marking failure. Conclusions CT-guided microcoil localization for pulmonary nodules is a safe and effective procedure. Small needle-pleura angle (<= 30 degrees), pleura-microcoil distance (<= 20 mm), and the presence of pleural indentation during the procedure are significant risk factors contributing to microcoil pleura marking failure.