Soil cracks significantly affect preferential flow; however, there are some uncertainties associated with the effect of soil cracks on preferential flow in karst areas in southwest China. In this study, ground-penetrating radar (GPR) was applied to pedons to investigate the soil crack properties (inclusion, width, and configuration). Blue dye tracing experiments were designed, based on geophysical detection results, to assess the influences of inclusions (sand grains and rock fragments), crack width (1, 1.5, and 2 cm), and configuration (I-shape, V-shape, and Λ-shape) on the preferential flow. Our results indicated that (1) GPR envelope can describe the configuration of isolated soil cracks; (2) the Brilliant Blue FCF (C.I. Food Blue 2) infiltration rate and depth were over 1.5 times slower and 1.2–3.8 times lower those of water, respectively, during infiltration; (3) soil cracks can accelerate infiltration and increase the maximum dye-penetration depth, cumulative infiltration, and wetting front depth by at least an average of 5.2% and 63.2%, respectively; and (4) the I- and Λ-shaped soil crack configurations contributed to preferential flow, while the flow was not observed along the V-shaped configuration crack pore paths. The I-shaped configurations, with a width of 1.5 cm, were filled with rock fragments and had higher preferential flow ratios (18.2%–52.3%) and length indexes (4.0%–33.8%) than those of other configurations. Inclusions, crack widths, and configurations had significant influences on preferential flow ( p < 0.05). The influence of soil crack properties on preferential flow cannot be neglected during vegetation restoration and groundwater security processes in karst areas.