Distribution patterns of ramet population of Iris japonica Thumb. and their effect on species diversity in the herb layer in three micro-habitats (open area of forest edge(OAFE), bamboo forest(BF) and evergreen broadleaved forest(EBF)) on Jinyun Mountain were studied using spatial pattern, niche and diversity analysis in a combination of population and community methods. The results were as follows: judged by V/m and Morisita index(Iδ), ramet population of I. japonica in three micro-habitats all clumped from scale 0.5 m×0.5 m to 2 m×2 m; the pattern scale and pattern intensity both gradually decreased in all scales and density of ramet population of I. japonica decreased with the increase in canopy density and the decrease in RPFD and R/FR from OAFE to EBF. In OAFE and BF, widespread I. japonica had a significantly negative influence on the dominance of original dominant species and on species diversity of the herb layer (p<0.05); however, those influences in EBF were extremely weak. The mechanisms that effect of pattern characteristics of I. japonica ramet population on species diversity of herb layer in three micro-habitats were different. In OAFE, high density and pattern intensity of I. japonica resulting from the open canopy which decreased the species diversity of the herb layer, especially for the richness of rare species, by means of strong regeneration niche (above-ground spatial niche and below-ground root niche) and trophic niche (nutrient) competition; in BF, moderate density and pattern intensity of I. japonica resulting from the bamboo canopy that had negative effect on the occurrence of rare species and on the survival of other herb species by means of strong regeneration niche (below-ground root niche) and trophic niche (above-ground for light and below-ground for nutrient) competition; in EBF, low density and pattern intensity resulting from the closed canopy which had little effect on the survival of herb species, because the random distribution of I. japonica caused by the low light in EBF lead to weak niche competition, just to trophic niche competition for nutrient. The pattern intensity and clonal growth of ramet population of I. japonica and soil status mainly determined by the canopy that have a significant influence on the intensity of regeneration niche (above-ground spatial niche and below-ground root niche) and trophic niche (above-ground for light and below-ground for nutrient) competition between I. japonica and other herb species, which is the determinant to the mechanism that effect of ramet population of I. japonica on species diversity of the herb layer.