As an important component of the new economy, e-commerce has become a significant force to promote the upgrading of consumption structure and to strengthen the supply-side structural reform. Therefore, corresponding to its rapid development, the absence of statistical system of electronic commerce has led to the lag of statistical work. This situation resulted in the lack of basic and authoritative statistical data in the process of industrial management. First of all, we review the related researches on e-commerce statistics in China. Then, according to the particularity of electronic commerce different from traditional industry statistics, we analyze the problem of its statistical organization system from the perspective of industry chain, discuss the problem of statistical boundaries based on its variety of activities, and discuss the construction and maintenance of the basic unit database, the innovation of e-commerce survey methods and the data quality management in the context of big data. Finally, we put forward some suggestions for the e-commerce statistical system, such as, the statistical organization system, the standardization of the statistical system, the certification system for electronic commerce, the publicity and law enforcement, and the application of big data in e-commerce statistics.