The moss-cyanobacteria association contributes nitrogen fixation that provides novel nitrogen inputs to nutrient-limited ecosystems, playing a non-negligible role in nitrogen cycling and ecological restoration within nitrogen-limited ecosystems. However, research remains scarce on the colonization characteristics (including cyanobacterial colonization rate and biomass) of cyanobacteria associated with epilithic mosses and their regulatory mechanisms in severely nitrogen-deficient degraded karst ecosystems. This study focuses on epilithic mosses, integrating their multidimensional functional traits (morphological, physiological, hydric and chemical characteristics) with environmental factors (karst rocky desertification degree, elevation, light intensity and UV-A radiation) to elucidate cyanobacterial colonization characteristics and identify the key drivers. Our results reveal high species diversity in the moss-cyanobacteria associations, with 37 moss species and 78 cyanobacterial species identified. Moss species identity, nitrogen (N) content, and pH emerged as critical determinants of cyanobacterial colonization. Notably, the degree of karst ecosystem degradation showed no significant negative impact on cyanobacterial colonization, whereas increasing elevation markedly reduced colonization rates. The widely distributed epilithic moss-cyanobacteria associations may exert positive influences on nitrogen cycling and rocky desertification restoration processes in degraded karst ecosystems. Moreover, elevation and moss chemical characteristics demonstrated stronger predictive capacity for cyanobacterial colonization than other environmental factors and moss traits. These findings elucidate key drivers of cyanobacterial colonization, providing insights for enhancing nitrogen cycling and guiding restoration strategies in degraded karst ecosystems.