Understanding the interaction between heterogeneous precipitates and grain boundaries (GBs) is of great significance for tailoring the stability and mechanical properties of nanograined materials. In this work, the nanoscale interaction between the cylindrical precipitate and the migrating GB is investigated by atomic simulation. The results show that the resistance for GB migration can be increased by decreasing the direction angle alpha (the angle between the axis of the precipitate and the tilt axis of GB). For the larger precipitate, the influence of direction angle is more pronounced. With the increase in shear strain, the interaction between the specific precipitate and GB changes the material deformation mechanism from "GB migration" to "GB migration accompanied with activated dislocations or GB deformation," which contributes to the softening of the material. By simultaneously tuning the direction angle and size of heterogeneous precipitates, the GB deformation can be strongly inhibited and the stability of GBs can be significantly improved.