Efficiently and accurately calculating the plasma transport process is one of the difficulties in aerospace plasma application simulation, especially in the magnetic sail spacecraft applications that have a huge size. This paper develops a three-dimensional trilinear anisotropic immersed-finite-element direct-implicit particle-in-cell (IFE-DIPIC) model to solve the problem of large-scale, long-term evolution plasma with complex interfaces. The model uses the DIPIC method to track the motion of particles in the plasma while simulating the anisotropic electric field containing an interface by using a modified trilinear anisotropic IFE method. Compared to the previous models, the developed model in this paper allows for the use of larger spatial and time steps in the Cartesian meshes without inducing numerical divergence. Using an interface-independent mesh avoids redundant interpolation in the PIC method, further improving efficiency. These advantages significantly improve the efficiency in solving actual complex three-dimensional plasma physics problems. The accuracy, efficiency, stability, and applicability of the proposed model are proved through numerical examples and the application in magnetic sail. The simulation results indicate that the developed model can efficiently simulate the actual working conditions of magnetic sails. The performance is significantly influenced by both the direction and magnitude of the magnetic moment.