By adopting SITC three digit trade data of 110 major countries, this paper calculates the export sophistication of 26 sub-sectors in manufacturing in China between 2002 and 2014. Then it measures the transformation of China’s trade structure and tests the influence of the dynamic changes in manufacturing factor structure on the trade structure. The findings are: firstly, the continuous upgrading of the factor structure has a significant role in promoting the transformation of trade structure, but the effect is different among different manufacturing sub-sectors. Secondly, the proportion of high-end factors in the export trade is relatively low, but the structure of factors has been gradually rationalized after the financial crisis. Thirdly, due to the impact of some factors such as industrial or export policies, the primary factors have crowding out effect on advanced ones, impeding the transformation of trade structure. Therefore, differentiated allocation of factors should be adopted in different industries to accord with the characteristics of the factor structure and to promote the factor structure upgrading.