This paper analyzes R&D efficiency changes of pharmaceutical industry by DEA-Malmquist on the basis of the selected panel data from 2002 to 2011. The paper indicates: In terms of time, TFP(total factor productivity) of entire pharmaceutical industry shows an increasing trend with year and overall average annual growth rate reach up to 5.7%, TFP and TC (technological progress index )curves are highly similar; technological progress is the main source to promote the growth of TFP; In terms of industry, TFP and TC values in different industries are all greater than 1 for the recent 10 years, the technical efficiency and TC play different role in TFP growth for different industries.