Abstract Mogao grottoes is famous for its exquisite murals, these murals were composed of pigment powders arranged in successive layers. The depth profile of these painted layers is a key information for studying mural diseases and providing a scientific basis of suitable restoration and conservation on the ancient murals. However, the depth profile was carried out only from cross-sectional analysis of mural fractions at present, which damaged murals and required complex measurements. Laser-induced breakdown spectroscopy (LIBS) was introduced for depth profile of painted layers owing to its multi-elemental capability, rapid, no preparation and the ability to resolve depth profiles of elemental composition. In this work, as one of the most commonly presented on Mogao murals, the green painted layers were investigated by LIBS technique. The color shades of different green areas were demonstrated with the pigment sizes, so it is essential to study the influence of pigment sizes on laser ablation depth for thickness analysis of the green layers. The simulated green layers composed of five different pigments sizes were prepared and analyzed by LIBS technique coupling with cross-section analysis, relationships of laser pulses and ablation depth in each pigment size fraction were obtained quantitatively. It was found that the average ablation rate (AAR) of laser pulse gradually become larger with decreasing of pigment sizes on green layers. The relationship can be used to achieve the measurements of green layer thicknesses in situ with using LIBS on Mogao murals.