Recently, unmanned aerial vehicles (UAVs) have attracted much attention due to their on-demand deployment, high mobility, and low cost. For UAVs navigating in an unknown environment, efficient environment representation is needed due to the storage limitation of the UAVs. Nonetheless, building an accurate and compact environment representation model is highly non-trivial because of the unknown shape of the obstacles and the time-consuming operations such as finding and eliminating the environmental details. To overcome these challenges, a novel vertical strip extraction algorithm is proposed to analyze the probability density function characteristics of the normalized disparity value and segment the obstacles through an adaptive size sliding window. In addition, a plane adjustment algorithm is proposed to represent the obstacle surfaces as polygonal prism profiles while minimizing the redundant obstacle information. By combining these two proposed algorithms, the depth sensor data can be converted into the multi-layer polygonal prism models in real time. Besides, a drone platform equipped with a depth sensor is developed to build the compact environment representation models in the real world. Experimental results demonstrate that the proposed scheme achieves better performance in terms of precision and storage as compared to the baseline.