The vegetation-soil system is fundamental to island ecosystem and changes considerably across sandy and rocky islands due to different natural and anthropogenic factors. An island chain, which is characterized by the coexistence of sandy and rocky islands, the connection of the islands by bridges, and complex influencing factors, was used as the study area. The vegetation-soil system was represented using different indicators and three newly-proposed indices, namely, vegetation health index (VHI), soil health index (SHI), and vegetation-soil system health index (VSSHI). The complex factors were identified in aspects of island basic factors, landscape pattern, terrain condition, and ecological indices. Then, the spatial responses of the system to the factors were analyzed at island and site scales. Results indicated that the vegetation-soil system showed similar and different responses to the complex factors across the dual scales. The similarity was represented by the higher sensitivities of VHI and VSSHI compared with that of SHI at both scales, and the difference mainly indicated that the influences of landscape pattern factors distinctly decreased along the scales from island to site. Island area, sea reclamation proportion, vegetation proportion, and natural ecosystem damaged index were the most important factors at island scale, while the ecological indices showed the highest influences at site scale. The study revealed the spatial characteristics of the vegetation-soil system across different types of islands, clarified the spatial responses of the system to complex factors at the dual scales, and identified the main influencing factors of the system.