Ultra-deep well perforation is an important direction for the development of unconventional oil and gas resources, the security with shock loads is a difficult technical problem. Firstly, the theoretical analysis of perforated string is carried out, the dynamics models of which are established in the directions of axial, radial and circumferential. Secondly, the process of perforating with hundreds of bullets is simulated by using the software of LS-DYNA (ANSYS, Inc, Pennsylvania, USA). The propagation attenuation model of shock loads is established, and a calculation model to predict shock loads at different positions of the tubing interval has been fitted by considering multiple factors. The dynamic response of perforated string is studied, and the vulnerable parts of which are found out. Thirdly, the optimization measures are put forward for ultra-deep well perforation by the design of shock adsorption and safety distance of the packer. Finally, the field case of an ultra-deep well shows that the research method in this paper is practical, and the optimization measures are reasonable and effective. This study can provide important guidance to reduce shock damage and improve security for ultra-deep well perforation.