Soil cracks significantly affect the preferential flow, and various uncertainties are associated with the effect of soil cracks on preferential flow in karst areas in Southwest China. This study investigated soil crack properties (inclusions, width, and configuration) by applying ground‐penetrating RADAR (GPR) to pedons. Blue dye‐tracing experiments were designed based on the geophysical detection results to assess the influences of crack inclusions (sand grains and rock fragments), crack widths (1, 1.5, and 2 cm), and configurations (I‐shape, V‐shape, and Λ‐shape) on preferential flow. The following results were obtained: (1) the GPR envelope can describe the configuration of isolated soil cracks; (2) soil cracks can accelerate infiltration and increase the maximum dye‐penetration depth, cumulative infiltration, and wetting‐front depth by averages of at least 5.2%, 63.2% and 4.4%, respectively; and (3) the I‐ and Λ‐shaped soil crack configurations contributed to preferential flow, but the preferential flow was not observed along the V‐shaped‐configuration‐crack pore paths despite the retardation of brilliant blue FCF. The I‐shaped configurations, with a crack width of 1.5 cm, were filled with rock fragments and had higher preferential flow ratios (18.2%–52.3%) and length indices (4.0%–33.8%) compared to the other configurations. In summary, inclusions, crack width, and configuration significantly influence the preferential flow (p < 0.05), and the influence of these soil crack properties on preferential flow cannot be neglected during vegetation restoration and groundwater security operations in karst areas.