Atomic resolution secondary electron imaging (ARSEI) has become an alternative tool for material characterization; however, its application potential is still underestimated due to insufficient understanding of the imaging mechanism. In this work, a robust quantum trajectory Monte Carlo method is developed to theoretically investigate the physical processes of ARSEI and thereby establish a new imaging mechanism. The new mechanism suggests that ARSEI can even identify the atoms of the same element in different atomic layers near the surface with a depth difference <2 Å. Thus, ARSEI can be expected to greatly promote the development of material characterization. For example, it may help to directly observe the AA, AB, and BA stacking in few-layer two-dimensional materials and to determine in which layer of a multilayer material an atom is adsorbed.