A waterproof keyboard structure and an assembly method thereof are provided. The waterproof keyboard structure includes a keyboard module, and a keyboard frame framing on the keyboard module, wherein an elastic waterproof layer is formed by means of double injection or insert molding on the keyboard frame. The keyboard module is defined with a key surface, and an assembly surface arranged opposite to the key surface. The elastic waterproof layer is clad on the key surface, and the keyboard module with the assembly surface facing a seat is assembled together with the keyboard frame in an accommodating space, thereby having the elastic waterproof layer closely fit with the seat to form a waterproof ring.