Desertification is the most severe problem in grasslands and sandlands in north China. In the desertified grassland, seed germination and seedling growth are affected by many ecological factors, such as drought, high temperature, sand burial, and wind and water erosion. In Inner Mongolia grassland of north China, sand burial is a common phenomenon caused by moving sand dunes. Plant shoots, seeds, and seedlings of sand dune plants are often buried by sand. Thus, plants must tolerate sand burial to survive and reproduce in sand dune habitats. Clonal plants, especially guerilla ones, can invade open patches through clonal growth, which may greatly affect soil nutrition status and microbial communities of the invaded sites. Previous study indicated that clonal growth and integration play an important role in their clonal expansion, such as in supporting the survival of new ramet on sand dunes. Psammochloa villosa produces linear monopodially growing rhizomes and it mainly relies on clonal growth to sustain and renew its populations. Hedysarum laeve is one of the arid-active and sand-fixation plants which can not only conserve soil, but also block the wind, reduce soil erosion, and thus maintain the balance and stability of arid areas. Dark septate endophytes (DSE), a miscellaneous group of ascomycetes, colonize root tissues intracellularly and intercellularly without causing apparent negative effects on the host plant. DSE fungi exhibit a broad range of host plants. DSE may benefit their host plants by facilitating the uptake of water and mineral nutrients from soil, and suppressing infection by plant pathogens. To investigate the effects of the growth of clonal plants on the activities of DSE and soil physical and chemical properties of invaded sites in Inner Mongolia, China, soil samples (0-50 cm depth) were collected under two guerilla-type, rhizomatous clonal plants, H. laeve and P. villosa, in June, August and October in 2013, respectively. The results showed that the clonal plants gradually invaded the bare spaces of community from June to October. The number of invaded community of P. villosa was higher than that of H. laeve. DSE colonization in roots of H. laeve community declined gradually with the sampling time. The highest colonization rate was found in roots sampled in June. In contrast, DSE colonization of P. villosa increased with the sampling time with the peak colonization rate in October. The invasion of clonal plants significantly increased the content of soil available nutrition, such as available N and P, which became more suitable for the growth of clonal plants. DSE colonization rate in H. laeve root systems in the bare spaces positively correlated with soil pH and electrical conductivity. Whilst for P. villosa, DSE colonization rate had strong negative correlation with soil pH, but had positive correlation with soil electrical conductivity, available N and available P, respectively. We concluded that the invasion of clonal plants greatly affected DSE colonization and soil nutrition status, although such effects varied between different clonal plants. Our findings showed that both clonal plant species enhanced the contents of available nutrients. Clonal plants were superior to non-clonal plants in terms of sand fixation, and greatly improved self-healing ability in adverse environments.