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Bacteria, fungi, and protist are important in driving nutrient cycling. The microbiological mechanism underlying vegetation restoration during different temperature and precipitation gradients remains unclear. To determine the relationship between microbes and nutrients, we examined the changes in soil bacterial, fungal, and protist diversity and community composition under two different temperatures in a plantation forest and shrubland as well as reference cropland in a karst region. Bacterial and protist diversity in the warm and low‐altitude region of Guangxi (average temperature 20.9°C) was higher in cropland than in shrubland or plantation forest. By contrast, fungal richness was lower in cropland than in shrubland. A co‐occurrence network revealed higher numbers of correlated links among the bacterial, fungal, and protist taxa in the cool and high‐altitude region of Guizhou (average temperature 14.6°C) than in the warm and low‐altitude region of Guangxi. Stronger interactions were observed among microbial taxa under cropland than in vegetation restoration. The protist groups Cercozoa and Lobosa showed the highest numbers of links with the bacterial phyla Acidobacteria and Proteobacteria and with the fungal phylum Ascomycota. The numbers of Proteobacteria, Ascomycota, and Cercozoa were most correlated with soil nutrient levels of carbon, nitrogen, and phosphorus. Overall, microbial interactions were higher at low temperatures than at high temperatures, consequently intensifying the predation of bacteria and fungi by protists at a low‐temperature level. Furthermore, Proteobacteria, Ascomycota, and Cercozoa were the keystone taxa linked to nutrient availability; hence, effective monitoring of these dominant groups may be beneficial for increasing nutrient accumulation during vegetation restoration. [ABSTRACT FROM AUTHOR]