Abstract: Combined with CDIO innovation mode, the paper explores High-tech innovation application talents of the multidisciplinary penetration intersection GIS training. Based on the establishment of talent training target, the modification of teaching plan and teaching outline, the cultivation of teachers and the teaching method reform, the author establishes innovative talents training mode of GIS in new era and explores the knowledge structure and ability structure of the innovative application of "3s" and the way of training GIS technology innovative talents.