Using PeakForce Tapping with its direct, pN level force control, we obtain high resolution images of the extremely fragile SEI layer formed upon cycling on the Si anode. This allows us to investigate the formation, evolution, and failure mechanisms of the SEI layer on patterned Si island structures, showing for the first time the in operando cracking of SEI layer. These results offer guidance for strategies to tailor passivation layers and thus address the key issue of cycling lifetime in higher capacity Li-ion batteries.