Abstract:The paper constructsan evaluation index system of scientific research efficiency in higher vocational colleges. By DEA method, 30 national higher vocational colleges’comprehensive scientific research efficiency from 2010 to 2015 is calculated. It is found that as time goes on, the gap between the provincial comprehensive scientific research efficiency values in higher vocational colleges presents U shape, and the efficiency gap in the last four years has gradually widened. According to DEA-Tobit model, it is found that the following four factors, that is economic development level, industrial structure, government-research-funding subsidy and industrial-academic-research cooperation, have significant positive influence on scientific research efficiency in higher vocational colleges, and regional education resources, regional population quality and enterprise technology spillover doesn’t pass the significance test.