Simulating the force-deformation behavior of stone masonry is a challenging issue. This paper contributes to this topic by developing a detailed micro-modeling method using extrinsic cohesive elements. To consider contact and friction, a new node-to-node algorithm is implemented in a finite element library with a parallel framework, which allows for high performance computing. To illustrate the application of this model, we calibrate our model with a diagonal compression test of stone masonry panel. To highlight the capabilities of the modeling approach, a series of parametric studies are conducted, which illustrate the influence of mortar-interface strength ratio and the spatial variation of material properties on the force-deformation response and the failure mechanism. The challenges related with the proposed framework, i.e., suitable calibration of the material parameters and direct comparison with experiments, are also pointed out.