For deeper understanding of the Sino-US trade war，effective evaluation of the level of intellectual property protection，innovation ability and trade structure is required. Based on the statistics of prefecture-level cities in Guangdong Province from 2006 to 2016，this report designs and calculates the intellectual property protection index，innovation ability index and trade structure index. Using the principal component analysis and descriptive statistical analysis，this paper finds out：First，the level of intellectual property protection，innovation ability and optimization degree of trade structure of the cities in the Pearl River Delta is at a high level in Guangdong Province，but it shows a downtrend in recent years. Second，the level of intellectual property protection，innovation ability and optimization degree of trade structure of the cities in eastern，western and northern Guangdong Province are weaker than that of the cities in the Pearl River Delta，but it is strengthening in recent years，at the same time，there is a narrowing trend in the gap of the three indicators between the cities of eastern，western and northern Guangdong Province and the cities in Pearl River Delta. Third，there is a certain correlation between the level of intellectual property protection，innovation ability and trade structure，among which the relationship between the level of intellectual property protection and the innovation ability is clearer. These results have provided statistical evidence for Guangdong Province for improvement of the level of intellectual property protection，innovation ability and trade structure.