The invention discloses a system precision processing method of a fragile transparent special-shaped 3D structure. The system precision processing method comprises the following steps of building a laser welding platform of the special-shaped 3D structure, wherein the platform comprises a laser, a laser path, a coaxial vision system, a paraxial vision system, a welding head, a clamp, a horizontalwelding bracket and a movement platform; clamping a sample by the clamp; mounting the clamp after clamping the sample to the movement platform, and adjusting the clamp by the coaxial vision system and the horizontal adjusting bracket; and grabbing a welding profile by the paraxial vision system to perform profile positioning and processing path planning; generating laser by the laser, and focusing the laser on a welding interface to be welded through the laser path and the welding head, and moving the movement platform according to the positioned profile and the planned processing path untilfinishing the welding; placing a welded sample in an annealing furnace, and annealing according to a temperature curve of heating, constant annealing temperature and cooling; and placing the annealedwelded sample in a reinforcing furnace to be reinforced.