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Protective layer mining is a safe and effective method of gas control in coal mining; we should pay more attention to changes in the pore structure of coal in protected layers, but there is less research in this aspect. We analyzed the characteristics of different-size pores in coal samples affected and unaffected by a protective layer at a distance of 900 m from the open-off cut of the protected layer. The pore morphology, type, size, and distribution in the coal seams affected and unaffected by the protective layer were qualitatively studied via field-emission scanning electron microscopy. Mercury intrusion capillary pressure testing was applied to analyze differences in pores of the same size between coal seams affected and unaffected by the protective layer. Protective layer mining increases the pore sizes of irregular pores. The protective layer has a large effect on various pores at different distances from the open-off cut. Within 100–700 m of the open-off cut of the protected layer, the upper protective layer mining promotes the conversion of 1–10 μm pores to 8–200 μm pores. When the distance from the open-off cut is less than 100 m, the upper protective layer mining facilitates the transformation of 10–100-nm pores into 100 nm to 10 μm pores. At distances of 100–900 m from the open-off cut, the porosity of pores with sizes from 10 nm to 200 μm increases markedly (with a maximum increase of 14%). The results of this study provide a theoretical foundation for designing a protective layer, evaluating its effect, and the research of gas seepage law and gas emission. [Display omitted] • The protected layer has various effects on different-scale pores. • The protective layer causes a 14% porosity increase for pores from 10 nm to 200 μm. • Irregular pores are formed by the high pressure extrusion of the overlying strata. • The coal seam floor is damaged in a trapezoidal shape by the upper protective layer. [ABSTRACT FROM AUTHOR]