The invention discloses a gas bottle positioning system of a CNG transport ship. The gas bottle positioning system of the CNG transport ship comprises gas bottle bases arranged at the bottom of a ship body and a keel which is arranged on the upper middle portion of the ship body and is connected with a ship board; by means of spherical flanges and conical hole seats on the gas bottle bases, the bottoms of gas bottles are limited in a swing manner; by means of binding belts and the keel, the middle portions of the gas bottles are limited; and by means of bin outlet pipes, the upper portions of the gas bottles penetrate a bin cover and are sealed, so that a structure that the gas bottles are vertically arranged is formed. The bottoms of the gas bottles are limited in the swing manner, the middles of the gas bottles are limited through the binding belts, and through a two-point limiting structure, adaptability swing adjustment can be carried out on the bottles according to jolting and swing of the ship body, so that the impact of the ship body to the gas bottles and the gas bottle supports is reduced, and safety of gas bottle positioning in the driving process of the CNG ship is improved.