3D modeling plays a significant role in many industrial applications that require geometry information for pose measurements, such as grasping, spraying, etc. Due to random pose changes in the workpieces on the production line, demand for online 3D modeling has increased and many researchers have focused on it. However, online 3D modeling has not been entirely determined due to the occlusion of uncertain dynamic objects that disturb the modeling process. In this study, we propose an online 3D modeling method under uncertain dynamic occlusion based on a binocular camera. Firstly, focusing on uncertain dynamic objects, a novel dynamic object segmentation method based on motion consistency constraints is proposed, which achieves segmentation by random sampling and poses hypotheses clustering without any prior knowledge about objects. Then, in order to better register the incomplete point cloud of each frame, an optimization method based on local constraints of overlapping view regions and a global loop closure is introduced. It establishes constraints in covisibility regions between adjacent frames to optimize the registration of each frame, and it also establishes them between the global closed-loop frames to jointly optimize the entire 3D model. Finally, a confirmatory experimental workspace is designed and built to verify and evaluate our method. Our method achieves online 3D modeling under uncertain dynamic occlusion and acquires an entire 3D model. The pose measurement results further reflect the effectiveness.