With the rapid development of network technology, global e-commerce enterprises are mushrooming, and corresponding economic behaviors such as investment, financing and mergers and acquisitions of e-commerce enterprises are constantly appearing. Therefore, it is very important to construct the value assessment system of e-commerce enterprises. This paper takes the characteristics and value of e-commerce enterprises as a starting point, and explores the value assessment of e-commerce enterprises based on the real option theory of Black-Scholes (B-S), which is a model with good applicability in market transactions. Not only can the model reduce the computational complexity of enterprise value, it can also improve the accuracy of value assessment, which is now an important reference for the value assessment of e-commerce enterprises in the era of big data.