Using 1996-2009 panel data of 25 countries, the paper analyzes the national innovation efficiency and its influencing factors by using super-efficiency DEA and DEA-Tobit two-step method. The major findings include: 1) Economic crisis has a negative impact on national innovation efficiency and total factor productivity for every country. Moreover, the decline of TFP is mostly caused by Technical regress; 2) China's national innovation efficiency remains at a low level and has overall downward trend during the study period. In addition, technology regress in China is serious; 3) The innovation activities of enterprises, universities and research institutions have significant and sustained effect on promoting national innovation efficiency, so their synergetic innovation is effective; 4) A country's macro tax rate has Laffer effect on the national innovation efficiency, high and low tax rates are not conducive to promoting national innovation efficiency.