The plastic behaviors of crystalline materials are induced by the evolution of a series of dislocations. Discrete dislocation dynamics (DDD) can be used to model plastic deformation by taking into account the nucleation, annihilation, motion of dislocations, and formation of jogs, junctions, networks, and other dislocation structures directly. As a result, it can be used to investigate the physical correlation between material microstructures, dislocation structures, and plastic responses. It can also model the intrinsic size effect of plastic behaviors at the micron/submicron scales. Since its modeling scale is much larger than that of the microscopic molecular dynamics but is smaller than that of the macroscopic finite element method (FEM), DDD plays a connecting link role in multiscale modeling. In the present manuscript, three categories of DDD schemes, i.e., the DDD-FEM superposition algorithm, the DDD-FEM direct coupling algorithm, and DDD-extended FEM (XFEM) coupling algorithm, are further developed and optimized. In the DDD-FEM superposition algorithm, the consideration of dislocation climb is specifically included to take into account the high-temperature effect. In the DDD-FEM direct coupling algorithm, the so-called virtual dislocations are introduced to distribute the Eigen plastic strain by dislocation evolution to the FEM module more appropriately, and a special scheme is developed to calculate the Peach-Koehler force on the dislocation efficiently. To model the problems with strong or weak interfaces (such as cracks, voids, particles, and grain boundaries), the scheme coupling the DDD and XFEM, which is not sensitive to the finite element mesh, is further developed carefully. Each of these three DDD schemes has its own special characteristics, and so they are suitable for solving different plastic problems. Based on these three kinds of DDD algorithms, the plastic deformation mechanisms of nickel-based superalloy, the damage and fracture behaviors of crystalline materials, and the size effect and microstructure dependency of heterogeneous crystalline materials have been investigated systematically. For the nickel-based superalloy, the dislocation mechanisms for the hardening responses, the abnormal yielding behavior with increasing temperature, the loading rate effect, the lattice misfit effect, and the crystalline orientation effect and the dislocation climb effect have been studied in detail. Based on these dislocation mechanisms and the special two-phase material microstructures, a crystal plasticity constitutive law informed by dislocation and microstructure mechanisms suitable for single crystal nickel-based superalloy was here developed. Further, the microvoid growth mechanism, the crack tip-microvoid interaction, the crack tip ratchetting responses, the crack shielding effect by dislocation, and the effect of crack-tip dislocation emission on crack growth have also been investigated systematically through DDD simulations. In addition, the plastic behavior, its size effect, and intrinsic dislocation mechanisms for materials with heterogeneous structures, such as particle-enhanced metal matrix composites, multilayered metallic films, and polycrystalline materials, have also been studied carefully using DDD models, especially at elevated temperature. This type of DDD research has facilitated better understanding of the intrinsic mechanisms of hardening response, cyclic plasticity, fracture, damage evolution, size effect, and microstructure dependency. DDD can be further used to study the plastic behaviors of crystals under the extreme environmental conditions, such as high temperature, high pressure, high loading rate (shocking), chemical erosion environment, and high neutron irradiation. DDD has recently become a powerful model of the behavior of metallic materials at microscale in a more physical manner than existing plasticity models.