To address the issues of laser-induced shadow pit in anti-reflective (AR) film, the characteristics of the micro-/nano-crater in AR films irradiated with different laser energies, and the effects of the crater on the film and the fused silica substrate were studied. The results indicate that craters may be present solely in the film layer, or both the film layer and the substrate. Precursors such as trace particles in the sol-gel solution may be the main factor causing the formation of micro-/nano-crater. Finally, two physical models are proposed based on the properties of craters. That is, (1) the heat absorption of precursors generates plasma micro-explosion, and (2) the effect of recoil momentum and confined plasma pressure. The processes and mechanisms of the crater formation are further elaborated.