The goal of this article is threefold: First, the theoretical background for a model-based framework of argumentation to describe and evaluate argumentative processes in science education is presented. Based on the general model-based perspective in cognitive science and the philosophy of science, it is proposed to understand arguments as reasons for the appropriateness of a theoretical model which explains a certain phenomenon. Argumentation is considered to be the process of the critical evaluation of such a model if necessary in relation to alternative models. Secondly, some methodological details are exemplified for the use of a model-based analysis in the concrete classroom context. Third, the application of the approach in comparison with other analytical models will be presented to demonstrate the explicatory power and depth of the model-based perspective. Primarily, the framework of Toulmin to structurally analyse arguments is contrasted with the approach presented here. It will be demonstrated how common methodological and theoretical problems in the context of Toulmin's framework can be overcome through a model-based perspective. Additionally, a second more complex argumentative sequence will also be analysed according to the invented analytical scheme to give a broader impression of its potential in practical use.