<p>The role of human activities in island biogeography is highlighted under the background of global changes, and humans interfere with the island biodiversity by introducing alien species, occupying natural habitats, and planting forests or crops. China’s islands are receiving increasing human interferences in different forms and intensities and provide natural laboratories for the study on island biogeography under varying human interference. The five inhabited islands with intermediate human interference in Miaodao Archipelago served as the study area. The island and site scales were employed to delineate the plant diversities, and influencing factors were collected by adequately considering the intermediate human interference, and three aspects of factors, i.e., natural, human, and ecological factors, were obtained. Then, the spatial sensitivities of island plant diversities to the factors were identified and quantified. The results indicated that the species richness on the five islands was intermediate compared with the remaining islands in the same archipelago and those in the other regions of China. Different island groups in the same archipelago shared the common characteristics in species composition and each island group had its own feature under the specific human interference. The island area, isolation, and population presented the highest influencing degrees on plant diversity spatial pattern from the perspective of island scale, while the slope, artificial landscape area, and soil available phosphorus exerted the highest influence degrees at site scale. Human activities with intermediate intensity exert positive effects on plant diversity at island scale through species introduction but negative effects at site scale through occupying the natural habitats.</p>