New agricultural systems are required to satisfy societal expectations such as higher quantity and quality of agricultural products, reducing environmental impacts, and more jobs. However, identifying and implementing more suitable agricultural systems is difficult due to conflicting objectives and to the wide diversity of scientific disciplines required to solve agricultural issues. Therefore, designing models to assess the sustainability of agricultural systems requires multicriteria decision aid methods. The French agronomist community has recently developed 11 hierarchical and qualitative models to assess sustainability using the DEXi decision aid software. Here, we give guidelines to help designers to build their own specific models. First, we present the principles and applications of the DEXi software. Then, we provide guidance on the following steps of model designing: (1) initial analysis and planning of the design process, (2) selection and hierarchy of sustainability criteria, (3) indicator selection and building, (4) parameterization, (5) evaluation, and (6) model dissemination and uses. We then discuss advantages and drawbacks of this kind of modeling formalism, the role of a participatory approach, and the main properties to consider during the design process.