The specially geological background of karst area has created complex and broken topography and developed various micro-geomorphology, which made it difficult for people to clearly understand the spatial heterogeneity and ecological stoichiometry characteristics of soil carbon, nitrogen and phosphorus. On the basis of field investigation, soil sampling and test results, the mixed effect model evaluation method combining coefficient of variation was introduced, and the spatial heterogeneity of soil carbon, nitrogen and phosphorus under different micro-geomorphic types and their eco-chemical measurement characteristics were revealed from two aspects:total amount (soil organic carbon, total nitrogen and total phosphorus) and effective amount (active organic carbon, available nitrogen and available phosphorus). The results show that:(1) The coupling interpretation degree of soil organic carbon, total nitrogen and total phosphorus to the ratio of carbon, nitrogen and phosphorus under different micro-geomorphic types is:earth flatland (91.09%) > gully (91.02%) > pit (84.63%) > stone cavern (80.17%) > crevice (73.20%), with the lowest spatial heterogeneity of soil surface and the highest stone crevice. (2) In terms of available state, the coupling explanation degree of active organic carbon, available nitrogen, available phosphorus and the ratio of carbon, nitrogen and phosphorus is characterized as followed:crevice (84%) > stone cavern (58.15%) > earth flatland (47.80%) > pit (44.06%) > gully (32.18%), which indicates that the spatial heterogeneity of soil active organic carbon, available nitrogen and available phosphorus in stone crevice micro-topography is the lowest. (3) The coefficient of variation of ecological stoichiometry of total soil carbon, nitrogen and phosphorus under different micro-geomorphic types are all above 50% (C/N 80%, C/P 53.57%, and N/P 69.33%). By revealing the spatial heterogeneity of total and available carbon, nitrogen and phosphorus in different micro-geomorphic soils and the characteristics of eco-chemistry, we can provide data and scientific reference for karst soil system management scheme and coping with global change and carbon neutralization.