While a defense system is being acquired using simulation-based acquisition (SBA), part of the system would be described as hybrid systems that have both discrete and continuous components. Also we need to quantify the benefits of SBA somehow in order to clearly determine them. In this paper we propose a method for cost estimation of hybrid system models that are specified based on a formalism for modeling and simulation. Existing estimation methods designed for discrete or continuous system models cannot be directly applied to the estimation since they leave the interaction between the components out of consideration. On the contrary the proposed method estimates the cost in a 'rough order of magnitude' manner through measuring discrete and continuous factors of a model as well as another factor of their correlation.