Abstract: Climate change and human disturbance will aggravate habitat fragmentation, resulting in the formation of a series of “habitat islands”. Considering interdune lowlands as the “habitat island”, this study selected 18 interdune lowlands with different sizes in active sand dunes of Horqin Sand Land, to explore the effect of “habitat island” size on plant species distribution pattern and propose different protocols of species diversity conservation. Plant species showed different sensitivities to habitat fragmentation: The type I species mainly distributed in small islands (such as Artemisia wudanica, Phragmites communis and Vicia amoena), the type II species mainly distributed in large islands (such as Lespedeza davurica and Eragrostis pilosai), the type III species mainly distributed in medium size islands (such as Chenopodium aristatum and Sophora flavescens), and type IV species distributed in all types of islands (e.g., salix gordejevii). For given total area of islands, both the total and meadow species richness were in order of the combination of medium size islands > the combination of different sizes of islands > the combination of large islands > the combination of small islands, while both the species richness of psammophyte and steppe species were in order of the combination of different sizes of islands > the combination of medium size islands > the combination of large islands > the combination of small islands. Therefore, exploring the effects of “habitat island” size on plant species diversity and its distribution pattern will provide theoretical basis for plant diversity conservation in semiarid sand dunes.