The effects of particle shape differences on binary mixture shear flows are investigated using the Discrete Element Method (DEM). The binary mixtures consist of frictionless rods and disks, which have the same volume but significantly different shapes. In the shear flows, stacking structures of rods and disks are formed. The effects of the composition of the mixture on the stacking are examined. It is found that the number fraction of stacking particles is smaller for the mixtures than for the monodisperse rods and disks. For binary mixtures with small particle shape differences, the mixture stresses are bounded by the stresses of the two corresponding monodisperse systems. However, for binary mixtures with large particle shape differences, the stresses of the mixtures can be larger than the stresses of the monodisperse systems at large solid volume fractions because larger differences in particle shape cause geometrical interference in packing, leading to stronger particle–particle interactions in the flow. The stresses in dense binary mixtures are found to be exponential functions of the order parameter, which is a measure of particle alignment. Based on the simulation results, an empirical expression for the bulk friction coefficient (ratio of the shear stress to normal stress) for dense binary flows is proposed by accounting for the effects of particle alignment and solid volume fraction.