Safe spacecraft navigation on small solar system bodies requires an accurate and high-resolution representation of the surface. This work develops a super-resolution mapping algorithm based on flash LiDAR measurements for unstructured terrain. It integrates a novel approach of processing multiple range values per pixel per measurement to increase the measurement redundancy and thus the map accuracy. The proposed algorithm is thus able to overcome the limitations of the low flash LiDAR resolution. Micro- and macro-motion strategies are recommended to guarantee subpixel displacements crucial for the super-resolution algorithm, and measurement constraints are introduced to ensure high measurement quality. Computational experiments based on an advanced Flash LiDAR model in a realistic simulation environment of comet 67P/Churyumov-Gerasimenko compare the resulting digital elevation model (DEM) with a baseline DEM and demonstrate the advantages of our algorithm.