Software as a Service (SaaS) is a new software delivery model. More and more companies are offering their software by following it. In contrast to earlier attempts of application service provisioning, the SaaS delivery model is focused on exploiting economies of scale by offering the same instance of an application to as many customers, i.e. supporting multi-tenants. As well understand, the delivery model of SaaS does not allow the SaaS vendor to develop and maintain a version of application code for each individual customer, SaaS applications have to be customizable to fulfill the varying functional and quality requirements of individual tenants. In this paper, we propose variability modeling based on metagraph support SaaS providers in managing the variability for configuration and customization of SaaS applications. This novel approach can systematically describe variability points and their relationships, and assure the quality of the configuration inputs made by the customers.