Soil saturated hydraulic conductivity (Ks) is one of the most important parameters that determine soil water redistribution. However, it is little known in a karst area with thin, discontinuous, and rocky soils. The purpose of this paper was to investigate the spatial variability of Ks and its influencing factors in a small karst catchment with high heterogeneity in southwest China. Undisturbed surface (0–10 cm) soil samples were collected with metal cylinders from an 80 m × 80 m grid for measuring Ks, bulk density (ρb), non-capillary porosity (NCP), and capillary porosity (CP). Disturbed surface samples were taken with a shovel to measure soil organic carbon (SOC) and rock fragment content (RC). Environmental factors including topographical location (slope and depression), land-use type (forestland, shrubland, shrub-grassland, and farmland), slope gradient, slope exposure, and elevation were investigated for each sampling point. The results showed that Ks value was relatively high (9.10 m/d) with a moderate variation, and had a strong spatial dependence (nugget/sill value = 0.06 %). NCP showed a very significantly (p < 0.01) positive correlation but ρb showed a very significantly negative correlation with Ks. RC and SOC had significantly (p < 0.05) positive correlations but CP had no obvious effect on Ks. This indicated that NCP and ρb were the dominant influencing factors of Ks in a karst area. The effects of topographical locations and land-use types on Ks were not significant (p > 0.05), but their interaction effects were significant. This suggested that the influencing factors were more complex and they should be considered together in a karst area. The mean Ks value was the lowest in the forestland on the hillslope and in the farmland in the depression, indicating where the surface runoff may appear easily. Such results could help to better understand the soil hydrological processes and contribute to the building of hydrological models in small karst catchments.