The invention provides a deep groove filling structure and a manufacturing method of the deep groove filling structure. The manufacturing method includes the steps of providing a substrate, sequentially forming a buried oxide layer and a semiconductor layer which are located on the substrate, forming lateral walls on the lateral wall body of the buried oxide layer and the lateral wall body of the semiconductor layer, using the lateral walls as masks, removing partial substrate materials in contact with the buried oxide layer in the substrate direction, forming a groove defined by the remain substrate, the buried oxide layer and the lateral walls, forming an intrinsic semiconductor layer in the groove, and forming an isolation structure at the position, where the the intrinsic semiconductor layer is formed, of the groove. The deep groove filling structure comprises the substrate, the buried oxide layer and the semiconductor layer, and the buried oxide layer and the semiconductor layer are sequentially located on the substrate. The groove extending to the position below the semiconductor layer is formed in the lateral wall of the substrate, and the intrinsic semiconductor layer is arranged in the groove. According to the deep groove filling structure and the manufacturing method of the deep groove filling structure, the output signal distortion problem can be solved.