Based on the researches and results of ecology security assessment and the protection of biological diversity home and abroad, this paper presents a review of the present state and application features of ecological research in the hotspots just talked about, which within the approaches of Geographic Information Systems (GIS for short) and Remote Sensing (RS for short) technology briefly. After that, this paper also generalizes and concludes the disadvantages of GIS and RS application in ecological security assessment and biodiversity conservation, on this basis, tries to explore the ecological integrated research framework and propose an extensible framework called Assembly-Line preliminary. Lastly, this paper discusses about the future of the integrated research of ecology with GIS and RS.