In this work, we investigate the microstructure and oxidation of Si nanopillars and report that the oxidation at the sidewall of Si pillars is initially retarded (the so-called self-limiting) and eventually stops altogether at a certain size (stopping size), and further oxidation causes cracks at the bottom of the pillars, that depends on the initial Si nanopillar diameter and the experimental conditions. The diffusion of oxidant in the oxide and the compressive stress due to volume expansion from Si to SiO2 caused by the old oxide are insufficient to explain the above phenomenon. Herein, the chemical reaction (breaking of Si-Si bonds) that causes the remaining Si-Si bonds to shrink is introduced; this new model well explains the oxidation of Si nanopillars with the evidence of the change in crystal planes distances observed from transmission electron microscope. The present work contributes to the intrinsic understanding and precise controlling of oxidation in Si nanopillars for future device fabrication.