E-commerce plays a significant role to grow its business globally by satisfying the modern consumer’s expectations. Without the help of Operating System (OS), e-commerce applications cannot be operated as well as broadcasted on the web. It is evident after analyzing this study that web administrators of the business are sometimes being careless, in some cases unaware about the risk of cyber-attack due the lack of vulnerability research on their OS. Therefore, a good number of the e-commerce applications are faced different type of OS exploitations through different types of attack e.g. denial of service, bypass, DECOVF, etc. that breaches the OS’s confidentiality, integrity and availability. In this paper, we analyzed 140 e-commerce sites servers’ information and its related 1138 vulnerabilities information to examine the risks and risky versions of the OS in e-commerce business. The probabilities of vulnerability are calculated using Orange 3 and feature selection operation has been performed using Weka through IBM statistical tool SPSS. This study identifies few versions of Ubuntu that are found in critical status in terms of risk position.