Aerial imagery has been increasingly adopted in mission-critical tasks, such as traffic surveillance, smart cities, and disaster assistance. However, identifying objects from aerial images faces the following challenges: 1) objects of interests are often too small and too dense relative to the images; 2) objects of interests are often in different relative sizes; and 3) the number of objects in each category is imbalanced. A novel network structure, Points Estimated Network (PENet), is proposed in this work to answer these challenges. PENet uses a Mask Resampling Module (MRM) to augment the imbalanced datasets, a coarse anchor-free detector (CPEN) to effectively predict the center points of the small object clusters, and a fine anchor-free detector FPEN to locate the precise positions of the small objects. An adaptive merge algorithm Non-maximum Merge (NMM) is implemented in CPEN to address the issue of detecting dense small objects, and a hierarchical loss is defined in FPEN to further improve the classification accuracy. Our extensive experiments on aerial datasets visDrone and UAVDT showed that PENet achieved higher precision results than existing state-of-the-art approaches. Our best model achieved 8.7% improvement on visDrone and 20.3% on UAVDT.