Two proof-of-concept batteries were designed and prepared for X-ray microtomography and radiography characterizations to investigate the degradation mechanisms of silicon (Si) based half cells during the first cycle. It is highlighted here for the first time that, apart from the significant volume expansion-induced pulverization, the electrochemical “deactivation” mechanism contributes significantly to the capacity loss during the first charge process. In addition, the unexpected electrochemically inactive Si particles are also believed to substantially decrease the energy density due to the inefficient utilization of loaded active material. These unexpected findings, which cannot be deduced from macroscopic electrochemical characterizations, expand the inherent explanations for performance deterioration of Si-anode material based lithium ion batteries (LIBs) and emphasize the vital value of microscopic techniques in revealing the correlation between macroscopic electrode structure and the overall electrochemical performance. •Two prototypes of lithium ion batteries were manufactured for micro X-ray imaging.•The first cycle of Si based half cells is investigated.•Volume change of electrochemically active Si particles are shown in 3D and 2D.•Electrochemical deactivation process is proved from the un-shifted X-ray attenuation.•Some of Si particles never experience the battery level electrochemical de/lithiation.