We present a method based on least-squares reverse time migration with plane-wave encoding (P-LSRTM) for rugged topography. Instead of modifying the wave field before migration, we modify the plane-wave encoding function and fill constant velocity to the area above rugged topography in the model so that P-LSRTM can be directly performed from rugged surface in the way same to shot domain reverse time migration. In order to improve efficiency and reduce I/O (input/output) cost, the dynamic encoding strategy and hybrid encoding strategy are implemented. Numerical test on SEG rugged topography model show that P-LSRTM can suppress migration artifacts in the migration image, and compensate amplitude in the middle-deep part efficiently. Without data correction, P-LSRTM can produce a satisfying image of near-surface if we could get an accurate near-surface velocity model. Moreover, the pre-stack P-LSRTM is more robust than conventional RTM in the presence of migration velocity errors.