The segmentation of pulmonary lobes is important in clinical assessment, lesion location, and surgical planning. Automatic lobe segmentation is challenging, mainly due to the incomplete fissures or the morphological variation resulting from lung disease. In this work, we propose a learning-based approach that incorporates information from the local fissures, the whole lung, and priori pulmonary anatomy knowledge to separate the lobes robustly and accurately. The prior pulmonary atlas is registered to the test CT images with the aid of the detected fissures. The result of the lobe segmentation is obtained by mapping the deformation function on the lobes-annotated atlas. The proposed method is evaluated in a custom dataset with COPD. Twenty-four CT scans randomly selected from the custom dataset were segmented manually and are available to the public. The experiments showed that the average dice coefficients were 0.95, 0.90, 0.97, 0.97, and 0.97, respectively, for the right upper, right middle, right lower, left upper, and left lower lobes. Moreover, the comparison of the performance with a former learning-based segmentation approach suggests that the presented method could achieve comparable segmentation accuracy and behave more robustly in cases with morphological specificity.