Stochastic characterization of radiation interaction is of importance to cell damage. Microdosimetry is to investigate the random structures of particle tracks in order to understand the dose-effect in cellular scales. In the review, we introduced the basic concepts of microdosimetry as well as the experimental methods (TEPC) and Monte Carlo simulations. Three basic biophysical models are interpreted and compared, including the target model, linear-quadratic model, and microdosimetric-kinetic model. The bottlenecks in the current microdosimetry research are also discussed, which need the interdisciplinary contributions from biology, physics, mathematics, computer science and electric engineering.