E-commerce is one of the industries most affected by big data, from collection to analytics in the highly competitive market. Previous research on big data analytics in E-commerce focused only on particular applications, and there is still a gap in presenting a framework to evaluate big data applications from a challenges-values point of view. This study employs a three-phase methodology to evaluate big data applications in E-commerce with respect to big data challenges and values using a hybrid multi-criteria decision-making technique that combines BWM and fuzzy TOPSIS. The results showed process challenge and the strategic value obtained the highest weight for challenges and values criteria. Financial fraud detection is relatively the most challenging, and online review analytics is the most valuable application of big data in E-commerce among identified applications. Evaluating big data applications based on cost and benefit criteria is practical for E-commerce managers and experts to make decisions on implementation priorities to overcome the challenges and make the most of values. Moreover, the proposed approach is not only limited to big data analytics in E-commerce and can also be applied in other industries to evaluate emerging technology applications.