Diazotrophs have potential for fixing atmospheric nitrogen (N) in terrestrial ecosystems. The effects of legumes on free-living N-fixing diazotrophs in the karst grassland were determined to provide a basis for ecosystem restoration. In a field experiment, diazotroph responses were examined in five treatments: control, low, and high densities of Amorpha fruticosa and Indigofera atropurpurea. The abundance and community composition of diazotrophs were significantly affected by sampling time and the interaction between different leguminous shrubs and planting density. Legume treatments significantly increased diazotroph abundance compared with the control in December (non-growing season). Greater N input with I. atropurpurea at high density in July (growing season) may suppress soil free-living N-fixing bacteria by decreasing diazotroph abundance. Diazotroph diversity was highest under I. atropurpurea in July. Phyllobacteriaceae and Beijerinckiaceae were abundant in the A. fruticosa plots, while Burkholderiaceae, Comamonadaceae, and Geobacteraceae were abundant in the I. atropurpurea plots. Regardless of the treatments, dissolved organic carbon was the key factor driving seasonal changes in diazotroph abundance and community composition. It suggests seasonal changes in temperature and soil moisture that drive nutrient availability (e.g., ammonium N and nitrate N) under planting legumes may explain the variation in diazotroph communities. Legumes reduced negative interactions among the species in network analyses. These findings suggest that increasing N availability by legume N fixation reduced inter-specific competition among the diazotrophs, with essential roles of rare taxa during the restoration of degraded lands in the karst region.