The fast charging process of high-pressure gas storage cylinders is accompanied by high temperature rise, which potentially induces the failure of solid materials inside the cylinders and the underfilling of the cylinders. A two-dimensional (2D) axisymmetric model simulated the charging process of hydrogen storage cylinders with a rated working pressure of 35 MPa and a volume of 150 L. During filling, the highest temperature rise inside the cylinder occurs at the bottom part of the cylinder, and the state of charge (SOC) is 46.4% after filling. This temperature rise can be reduced by precooling the injected hydrogen, and the highest SOC can reach 95.7% after injection. The SOC in the cylinder gradually increases with a decrease in the temperature of the hydrogen injection. The maximum SOC increase is 49.3%. For safety and the SOC exceeding 90%, the hydrogen gas should be precooled to below −10 °C, and the SOC could achieve more than 90.3%. The internal structure of the hydrogen cylinder was further optimized without a precooling condition. The selected length ratios were 25%, 50%, and 75%. Compared with the initial scheme, the SOC in the optimization scheme increased by 16%, 38.7%, and 40.1%.