The rationality evolution of China’s import and export commodity structure has been empirically estimated based on the input-output model and latest national economic input-output table. The study finds that the decreasing amplitude of China’s import commodity structure is smaller than export’s decreasing amplitude. The influence coefficient of machinery manufacturing, metal manufacturing, chemical industry, building industry, textile and leather manufacturing is relatively stable. The pulling effect of non-metal and mineral products industry on China’s economy is growing increasingly. The driving force coefficient of mining industry gets a rapid growth and ranks first of all industries. The rank disaccord between driving force coefficient and proportion of imports is more serious than that of exports. The chemical industry, machinery manufacturing and metal manufacturing industry undertake two kinds of tasks of pillar and bottleneck industry. The countermeasures for reducing import propitiation of machinery manufacturing goods, increasing mining and chemical industry imports, reinforcing export propitiation of chemical and metal manufacturing, encouraging enterprises to track leading technology in pillar and bottleneck industry are given in the paper