The multi-level body composition analysis pipeline takes 3D chest LDCT volume as input, identifies the 2D axial slices corresponding to T5, T8 and T10 vertebral levels, and segments cross-sectional region of each BC components on each level. For quality control, we design procedures to improve segmentation quality, assess tissue cropping and automatically identify failure cases. Time-to-event analysis on lung cancer incidence shows association between measured body composition components and lung cancer risks.