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This paper will focus on the generation of a three-dimensional GIS map by integration of image data and topographical data. The remote sensing platform in this research was an unmanned helicopter which is a low altitude-flying rotorcraft. An imaging sensor and a laser range finder were mounted on this helicopter. Because an RTK-GPS and a posture sensor were installed in the helicopter, the field topography can be generated by the laser data. In this research, we developed the method that the image data can be transformed to global coordinate integrating the topographic map. The developed system can generate a field map even if a field has some inclinations. The field test was carried out to evaluate the topographic error and the image mapping error. Consequently, the developed system could generate a topographic map with 9 cm error, and three-dimensional mapping error was 41 cm. Finally, the three-dimensional GIS map regarding NDVI was generated using the developed system.