Based on DEA-Malmquist index to measure total factor productivity index throughout each province and municipality, the paper analyses the technical efficiency index and the technological progress index from 2009 to 2012 in various provinces and cities, compares the value of the total factor productivity index of Henan Province to the average of six provinces in Central China and the nation, evaluates Henan province science and technology resource allocation efficiency; at the same time, based on the data of the relevant science and technology from 2010 to 2013,the paper evaluates the allocation efficiency of science and technology resources in Henan province of the prefecture level city, analyses that the elements of science and technology in Henan province are invested increasing continuously, but the structure is unreasonable, the ability of original innovation and basic conditions is a little weak, the management level and technical level is not high, and finally puts forward some policy suggestions for the government and the main body of science and technology.