A waterproof structure for an implanted electronic device is capable of preventing the liquid or moist from entering and damaging the circuit board of the electronic device. The waterproof structure includes a shell, a first material layer, a second material layer, and a third material layer. The first material layer covers at least a part of the implanted electronic device. The second material layer covers the first material layer. The internal space of the shell is configured for accommodating the implanted electronic device. The shell is made of PEEK (polyether ether ketone). The third material layer is disposed between the second material layer and the shell.