The 3-D automatic target recognition (ATR) has many advantages over its 2-D counterpart, but there are several constraints in the context of small low-cost unmanned aerial vehicles (UAVs). These limitations include the requirement for active rather than passive monitoring, high equipment costs, sensor packaging size, and processing burden. We, therefore, propose a new structure from motion (SfM) 3-D ATR architecture that exploits the UAV's onboard sensors, i.e., the visual band camera, gyroscope, and accelerometer, and meets the requirements of a small UAV system. We tested the proposed 3-D SfM ATR using simulated UAV reconnaissance scenarios and found that the performance was better than classic 3-D light detection and ranging (LIDAR) ATR, combining the advantages of 3-D LIDAR ATR and passive 2-D ATR. The main advantages of the proposed architecture include the rapid processing, target pose invariance, small template size, passive scene sensing, and inexpensive equipment. We implemented the SfM module under two keypoint detection, description and matching schemes, with the 3-D ATR module exploiting several current techniques. By comparing SfM 3-D ATR, 3-D LIDAR ATR, and 2-D ATR, we confirmed the superior performance of our new architecture.