Clintonia udensis is a perennial herb possessing two cytotypes diploid (2n=14) and tetraploid (4n=28). In the Hualongshan Mountains, the diploid of C. udensis primarily grows in 2450 m areas on the south slopes, while the tetraploid grows mainly in 1900 m areas on the north slopes. So, this intra-polyploidy is regarded as an excellent material to study the origination, evolution and adaption of plant polyploidy. Through field investigations and molecular genotyping, we initially analyzed the bud bank spatial characteristics, clonal growth, and spatial genetic structure populations between the different ploidy of C. udensis. It found that the rhizome knot styles of C. udensis had zigzag, C, V, and Y models between the two cytotypes. There was no dominated clone present in the diploid or tetraploid. The clone architectures of two ploidies were both phalanxes. However, the number of rhizome knots, the number of buds of each rhizome knot, the ratio of rhizome branches, and average tetraploid clones were higher than that of the diploid. The diversity indices of the tetraploid, such as clone diversity index, genetic distribution uniformity, and genetic diversity index, were also slightly higher than that of the diploid. Thus, clonal reproduction differentiation and significant genetic variations occurred between the diploid and tetraploid of C. udensis. These two cytotypes, through seed reproduction and clonal growth, became a facultative clonal species and maintained its survival stability and reproduction. During the evolutionary process, the tetraploid of C. udensis with higher clonal diversity and genetic diversity responded and adapted to new surroundings that different from the ancestral diploid in the Hualongshan Mountains.