This paper presents a method for occluded object based motion estimation and tracking system in dynamic image sequences using particle filter with 3D reconstruction. A unique characteristic of this study is its ability to cope with partial occlusion based continuous motion estimation using particle filter inspired from the mirror neuron system in human brain. To update a prior knowledge about the shape or motion of objects, firstly, fundamental 3D reconstruction based occlusion tracing method is applied and object landmarks are determined. And optical flow based motion vector is estimated from the movement of the landmarks. When arbitrary partial occlusions are occurred, the continuous motion of the hidden parts of object can be estimated by particle filter with optical flow. The resistance of the resulting estimation to partial occlusions enables the more accurate detection and handling of more severe occlusions.