Although the ecosystem extends numerous functions for the benefit of humankind, construction of horticultural facilities can potentially lead to the degeneration of some of these functions owing to the expansion of impervious regions and loss of habitats. Thus, this study aimed to examine the effect of construction of horticultural facilities on plant biodiversity. Analysis of the vegetation distribution characteristics showed that horticultural facilities had significantly lower plant diversity than did rice paddies. Hence, the proposed approach involved low-impact development, arrangement of habitat space, plant preservation, restricted use of chemical fertilizer, habitat creation, and reduced preservation cost. Lifestyle analysis suggested the importance of developing favorable environments for the growth of annual plants and aquatic plants. In all, 20 species of naturalized plants belonging to 10 families were identified. Furthermore, the proportion of these naturalized plants was higher in glass greenhouses and multi-span greenhouses, suggesting the advantages of employing natural soil mulching while avoiding concrete mulching. Statistical analysis was performed to validate the results, which suggested that impervious regions be converted to natural soils. Collectively, the findings of this study are expected to be used for establishing policies for the construction of eco-friendly and ecological horticultural facilities; this may aid the maintenance of sustainable agricultural landscapes and large-scale development of the reclaimed lands.