Software Product Line Engineering (SPLE) is a well-known method among software engineers in accommodating the need of creating a diversity of new software products based on reusable concept, mainly at component level including features. Besides, this method has proven to be useful for improving the quality of a software product in a fast and efficient way, by selecting the best match features in order to fulfill the specified goal of the product. However, selecting the features becomes a new problem, because there must be another method or approach to support it. On the structure of choice, weighted hypergraph is applied for determining a set of alternative features. To demonstrate how the proposed idea works, E-Learning product line is chosen as the SPLE problem. Conceptually, hypergraph is a generalization of regular graph, where each of its edges can connect more than two vertices. Along with the idea of k-way partitioning, this particular structure is utilized for providing a means for dividing features into three given quality attributes: security, usability, and reliability. In practice, each arc is associated with a certain weight in order to obtain several combinations of features. To conclude, by using a set of hypergraph with respective proper weight values, the proposed method produces a set of alternative features. This very recommendation can be taken into consideration by any software engineers who have same interest in E-Learning Product Line. Precisely, the recommendation covers 8 combinations of security feature, 4 combinations of usability feature and 8 combinations of reliability feature.