The problems of existing long underwater tunnels, i.e. Jiaozhou Bay Tunnel in Qingdao and Xiang’an Tunnel in Xiamen, are studied by theoretical analysis method and numerical calculation method. The designs of keys of drainage system, i.e. tunnel waterproofing, pump selection, pipe system arrangement, water hammer protection and sump volume, are analyzed. Suggestions are given as follows: 1) The water leakage of long underwater tunnel structure should be controlled strictly, and the full waterproofing method should be used. 2) The submersible pump with high corrosion resistance should be used as waste water pump. 3) The “one pipe two pumps” scheme for drainage system is the best; and there should not be more than 3 pumps in one pipe. 4) The water hammer eliminator should be used, and water hammer protection methods should be adopted as well. 5) The effective volume of sump should be decided according to risk analysis.