To simulate ballast performance accurately and efficiently, the input in discrete element models should be carefully selected, including the contact model and applied particle shape. To study the effects of the contact model and applied particle shape on the ballast performance (shear strength and deformation), the direct shear test (DST) model and the large-scale process simulation test (LPST) model were developed on the basis of two types of contact models, namely the rolling resistance linear (RRL) model and the linear contact (LC) model. Particle shapes are differentiated by clumps. A clump is a sphere assembly for one ballast particle. The results show that compared with the typical LC model, the RRL method is more efficient and realistic to predict shear strength results of ballast assemblies in DSTs. In addition, the RRL contact model can also provide accurate vertical and lateral ballast deformation under the cyclic loading in LPSTs.