Biocrusts are ecosystem engineers providing vital functions and services on the Earth's land surface, while biocrust ecology in degraded karst landscapes has not yet been well understood. Herein, we aim to address this research gap by comparing the differences of soil nutrients, extracellular enzyme activities, and microbial communities between intact crusts and moss-free crusts in a degraded ecosystem located in the center of contiguous karst areas of southwest China. The results showed that, one year after the removal of biocrust-forming mosses, soil nutrient contents (soil organic carbon, total nitrogen, total phosphorus, nitrate, and ammonium) and enzyme activities (soil β-glucosidase, sucrose, and urease) significantly declined in comparison with intact crusts. The removal of biocrust-forming mosses remarkably reduced total biomass, diversity and abundance of soil bacterial communities, and altered bacterial community structure, other than those of fungal communities. Moreover, the removal of biocrust-forming mosses resulted in a sharp decrease in the size and complexity of bacterial networks but slightly decreased those of fungal networks. Results of microbial communities indicated that soil bacteria were more responsive than fungi to the removal of biocrust-forming mosses and could be an indicator of disturbance to moss biocrusts in degraded karst areas. Overall, these findings highlight the importance of saving moss biocrusts as hotspots of ecosystem functioning and precious microbial genetic resources in degraded karst landscapes and promote a better understanding of biocrust ecology in humid climates under global change scenarios.