Karst collapse column, as a special geological body with chaotic internal structure, is easy to be a vertical water channel under the coal floor. Thus it is a major potential safety hazard in Carboniferous coalfield of North China Permo. The water channels in collapse column under the coal floor are composed of collapse column and floor water-conductive fissure zone. To investigate the mutation mechanism of seepage in the hidden collapse column, a broken rock permeability test system is independently developed. A series of experiments is conducted to examine the seepage in the collapse column under different floor damage conditions. Experimental results show that: the fundamental reason of the seepage mutation is caused by the changes of broken rock pore structures resulting from the large particle loss. The flow velocity increases with the increase of the pore diameter at the seepage boundary, and the initial porosity of the sample is higher than 0.21 when the seepage mutation occurs. The seepage boundaries have negligible effect on seepage without the occurrence of seepage mutation. The permeability of the sample increases with the increase of its porosity, and there is a power function relation between permeability ratio and porosity ratio. The negative non-Darcy factor is a sufficient and necessary conditions for the occurrence of seepage mutation, and the non-Darcy factor controls the degree of the seepage mutation intensity.