Coarse-grained soil is a commonly used material in earth-rock dams and soft foundation projects. An accurate understanding of its permeability characteristics is crucial to the safe design of the associated projects. Due to the scale effect, the outcomes of indoor percolation tests on scaled soils often do not accurately represent the permeability characteristics of coarse-grained soils with their original gradation. According to the previous studies, the scale effect of downsized soil materials is mainly affected by the maximum particle diameter dmax and the gradation structure of the particles, where the gradation structure can be expressed by the gradation area S. By changing dmax and S, 18 groups of graded soil materials are designed. Afterward, indoor permeability tests are conducted on each group of soil materials using a coarse-grained soil vertical penetrometer. The quantitative study of the influence of the scale effect on the permeability coefficient of coarse-grained soils is conducted, and a method for eliminating this effect is discussed. The test results show that: As a constant dmax, the permeability coefficient k decreases with increasing S, exhibiting an exponential relationship. At a constant S, the permeability coefficient k increases with increasing dmax, exhibiting a logarithmic relationship. The test results are utilized to formulate a quantitative model describing the influence of gradation on the permeability coefficient k. The feasibility of this calculation model is confirmed by applying it to existing results. Finally, a method for predicting the permeability properties of coarse-grained soils in their original gradation is proposed based on indoor permeability tests.