Type II storage vessel, which consists of a metallic liner hoop wrapped with a carbon fiber-resin composite to work at high pressure, has been widely adopted as the fuel container for compressed natural gas (CNG) vehicles. The general vessel, manufactured by welding enclosures to an open-end cylinder, shows uniform thickness throughout the whole liner, while the high pressure vessel, fabricated by the deep drawing and ironing (D.D.I) and spinning processes, has the integral junction part of cylinder with increased 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 is used to enhance fracture performance and fatigue life of the vessel, and variations of stress behaviors in the liner and composite were analyzed during the autofrettage process. The 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 the end closure, the stress distribution considering thickness variation was compared with that with uniform thickness, and the maximum inner capacity objective 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. Theoretical equivalent stresses were compared with those from the simulations, and the technique of FEM was verified.