Digital economy has been developing rapidly in Guangdong Province，with the digital economy scale is ranked first in China.Basing on the background of economic development，we measure the digital economic innovation level of 21 cities in Guangdong province from the comprehensive innovation and the average innovation level.Then we calculate the ranking of digital enterprises number，ranking of comprehensive innovation level，ranking of cycle innovation level and ranking of continuous innovation level according to the innovation index.At the same time，we observe the top five districts and counties in each city based on dimension of the three economic zones，one core，one belt and one zone.Finally，we use the quartile analysis method to comprehensively evaluate the innovation level of the digital economy.The main results are following as：1.the number of enterprises is not the key factor determining the level of regional digital economy innovation，and it is more closely related to the scientific and technological innovation activities of enterprises and digital economy innovation activities.2.The average innovation level of digital economy enterprises in a city is not closely related to the region where the city is located，but mainly highlights the close relationship between digital economy innovation policies and the leading enterprises of enterprise innovation.3.Per capita GDP is positively correlated with the innovation level of digital economy in general，and the positive correlation becomes more obvious when per capita GDP exceeds 200，000 yuan.