Most studies on island biogeography have focused on the terrestrial taxa; however, there are few studies on the drivers of diversity and community structure of intertidal organisms on islands. We evaluated the effect of landscape and marine environmental factors on the species richness (SR), functional diversity (FD), and community structure (SES.MFD) of intertidal invertebrates among the overall, inhabited, and uninhabited islands. Using the data on the intertidal organisms from 78 islands in South Korea, we implemented variable selection and piecewise structural equation modeling to determine the causal relationships between the SR, FD, and SES.MFD with four landscapes (i.e., island area, coastline length, distance from the mainland, and structural connectivity) and three marine environment factors (i.e., mean annual sea surface temperature variation, wind speed, and evapotranspiration). The coastline length had a positive effect on the SR and SES.MFD in the overall islands including inhabited and uninhabited islands. The SR and FD were negatively affected by the variation in sea surface temperature. The relative importance of the landscape and marine environmental factors differed between the inhabited and uninhabited islands. That is, the inhabited islands were mainly affected by the coastline length, whereas uninhabited islands were regulated by marine environmental factors. Our results demonstrated that the biotic factors of the island intertidal ecosystems are controlled by the interactions between the biotic and various environmental factors. Moreover, the results emphasize that the water stress on the intertidal organisms due to climate change may lead to a loss of biodiversity and functional clustering.