The present invention provides an etching method of a glass substrate and a wet etching apparatus thereof. The etching method of the glass substrate comprises steps of: providing a glass substrate (1) to be etched, a wet bench (3), etchants and a supply line (7); setting a tank (9) in the wet bench (3); filling in the tank (9) with a predetermined amount of the etchants through the supply line (7); delivering the glass substrate (1) to be etched into the wet bench (3); raising the tank (9) until the glass substrate (1) is completely immersed with the etchants in the tank (9); lowering the tank (9) to expose the glass substrate (1) after a predetermined soaking time. The etching method of the glass substrate is simple and easy for operation. It is capable of shortening the etching process time and raising the production efficiency.