Type II storage vessel, which consists of liner hoop wrapped with a carbon fibre-resin composite to work at high pressure, has been widely adopted as the fuel container for CNG vehicles. The general vessel, manufactured by welding to connect open-end cylinder with end closures, shows uniform thickness throughout the whole liner, while the high pressure vessel, fabricated by the D.D.I. and spinning processes, has the integral junction of cylinder and ends and shows increment of the end thickness along the meridian direction. This study established a design method for improvement of failure resistance and inner capacity of the seamless CNG pressure vessel (Type II) through finite element analysis with consideration of thickness variation. Autofrettage pressure to enhance fracture performance and fatigue life of the vessel was suggested, and variations of stress behaviors in the liner and composite were analyzed during the autofrettage process, and influence of the composite on generation of compressive residual stress was investigated. In order to verify advantages of the D. D. I. and the spinning processes for structural safety at end, the stress distribution considering thickness variation was compared with that with uniform thickness, and maximum inner capacity satisfying structural reliability was obtained. The inner capacity of the proposed model with the ratio of major axis to minor axis, 2.2, was expanded by 4.5%, compared to the existing one, and theoretical equivalent stresses were compared with those from the simulations, and the technique of FEM was verified.