In recent years, cloud computing, Internet of Things, mobile Internet and other emerging technologies have emerged and developed continuously, prompting various kinds of data to gradually show an explosive growth trend, and the resulting impact has penetrated into all levels of industry, scientific research, education, family and society, which marks that mankind has entered the era of big data comprehensively. At the same time, with the arrival of the era of big data, the concept of decarbonizing and greening of the supply chain is deeply rooted in the hearts of people, and it has become an inevitable trend for enterprises to promote the development and innovation of green supply chain. The supply chain of e-commerce is inseparable from big data technology. This paper intends to effectively combine low carbon economy and e-commerce from the perspective of big data-based application, and explore the green supply chain innovation management strategy based on the combination of low carbon economy and e-commerce under big data technology, so as to effectively promote the innovation and development of green supply chain management strategy in the era of low carbon economy.