The heatshield of ShenZhou spacecraft is mainly composed of FRP honeycomb sandwich structure. Aiming at the problem that the hole position accuracy is difficult to guarantee due to the clamping deformation, the process optimization and improvement are carried out. The tooling structure, clamping method, process flow and drilling equipment are improved. The test results show that the drilling accuracy can be effectively improved by adopting the low stress clamping method, reducing the turnover times and using the numerical control processing equipment.