Based on the relevant data of 13 prefecture-level cities in Hunan Province from 2006 to 2015, by using the DEA-BCC model and the Malmquist index model, an empirical study has been made on their innovation efficiency. The research results show that, from 2006 to 2015, there are two peaks in Hunan Province's innovation efficiency: (2008—2009) and (2010—2011) and two valley points: (2009—2010) and (2012—2013), characterized with an overall growth trend, with its average growth rate being 3.8%, mainly due to technological progress (2.0%) and scale efficiency (1.4%) growth. According to the innovation features of every individual city, the average comprehensive efficiency among them reaches 0.738, with a great diversity in their specific innovation efficiency. Changsha, Zhuzhou and Changde are ranked among DEA valid cities, while other cities in Hunan province belong to DEA invalid cities. The evaluation of innovation efficiency in Hunan Province and the evaluation results of innovation efficiency in various cities indicate that the level of innovation efficiency needs to be improved, with its major reliance on technological progress and scale effect.