This research proposes a UAV-based urban heat island effect space innovative remote sensing system that integrates UAV, IoT sensing, transmission device, and cloud platform applications. It is easy to obtain parts, relatively low price, and easy to assemble. Its innovation complements the limitations of the data measurement methods of UHI in the past. With its characteristics of spatial mobility and data continuity. It breaks through the limitation of thermal environment data that cannot measure the vertical structure of urban heat islands in the past and performs automatic environmental data collection, transmission, and storage with high precision and high sampling frequency. After the system is completed, field data collection and analysis are used to verify the system’s feasibility and discuss the existing limitations. This system is used by urban planning experts to measure the vertical space temperature and humidity of different surface pavements in Kinmen County, ROC. The measurement results have proved the feasibility and applicability of this system. It is a stable and high-precision innovative remote sensing system for the new urban heat island space.