A reciprocal transplant-replant experiment was carried out to investigate the clonal plasticity and local specialization of OAFE population (O type) and BF population (U type) of a clonal rhizome herb Iris japonica in contrasting reciprocal heterogeneous habitats on Jinyun Mountain. U Population had better performance of plant size and clonal propagation (including allocation to clonal propagation, daughter ramet and fine rhizome) in different reciprocal heterogeneous habitats than O population. Both the population origin and reciprocal spatial heterogeneous habitat had effects on clonal ramets and biomass of clonal components of experimental plants. The plasticity of clonal growth had difference in clonal components to balance High light-Low soil resources (water) (HL) or Low light-High soil resources (LH) due to the ecological isolation of the two I. japonica populations. Our findings indicated that two major types of patterns of spatial covariance of resources can have different effects on the growth and local variation of clonal plants.