This paper measures the comprehensive development of China’s cross-border e-commerce in the comprehensive pilot area in 2016 regarding the foundation ability level, service support level and potential development level. The result shows that 13 China’ cross-border e-commerce comprehensive pilot area can be divided into three parts, which have significant different comprehensive development levels. From the perspective of development process, the growth of the comprehensive development of the first part is slowing down, but the comprehensive development of the second part and the third part are still on the fast-rise, and the main drive of their rise is the growth of service support level. In addition, from the perspective of region, the comprehensive development levels present regional characteristics, economic characteristics and reverse cluster characteristics. Finally, based on the above conclusion, the paper puts forward corresponding policy suggestions.