Data envelopment analysis (DEA) based on mathematical programming model, is a good analysis method used to measure the relative efficiency of Decision Making Units (DMUs) with multiple inputs and multiple outputs. DEA-Malmquist productivity index measures the productivity change over time. The DEA-Malmquist productivity index can be decomposed into two components: one measuring the technical change and the other measuring the frontier shift. By using the DEA-Malmquist index analysis approach, this paper conducts an empirical study to evaluate the innovational productivity of China pharmaceutical manufacturing industry from the following two perspectives: twenty -three provincial regions and fifty-seven comprehensive economic zones with the time series data from 2001 to 2011. It deeply analyses the patent innovation efficiency change in different periods and analyses the technical change rate.