Rock outcrops are frequently visible in terrestrial landscapes, typically in karst. However, there has been insufficient research conducted on their effects on the formation of soil water and nutrients heterogeneity in nearby soil patches. In: 1) a rock desertification ecosystem, 2) an anthropogenic forest ecosystem, and 3) a secondary forest ecosystem in Shilin, Southwest China, rock occupancy ratio was measured, water received by and subsequently funneled off by rock outcrops was quantified, and their concentrations of the total organic carbon, nitrogen, phosphorus, and potassium were determined. Receiving rate R-r of those elements of the remaining soil patches in various 2 m x 2 m soil + rock outcrop samples were calculated, and r(200) at which R-r of the remaining soil patch was twice that without rock emergence was calculated to evaluate the heterogeneity difference among different elements in different ecosystems. There were 1.43-5.44 folds differences between R-r under the highest rock ratio (79.4%) sample and the rate of non-rock emergence sample for water, organic carbon, nitrogen, phosphorus, and potassium in the three ecosystems respectively, indicating a large supply heterogeneity for those elements within an ecosystem and between ecosystems. The r(200) were between 47% (water, at rock desertification ecosystem) to 90% (potassium at rock desertification ecosystem, depending on the receiving rate and funneling rate of the rock for different element in different ecosystem. In conclusion, large supply heterogeneity has derived from high variation of rock runoff determined by rock emergency ratio, the rate of receiving and the rate of funneling off by the rock. Our study provided new evidence to trace soil and water heterogeneity of microhabitats in rocky ecosystems. Additionally, rock outcrop is also an important factor in evaluating hydrological and related nutrient characteristics in rocky ecosystems.