N-doped microporous activated carbons were synthesized by hydrothermal doping with ammonia as the nitrogen precursor; the chemical, structural, and hydrogen storage properties of the developed activated carbons (ACs) were also examined. The results showed that this method is an effective way of preparing microporous activated carbons with high surface area. Both the surface areas and the N contents of ACs were increased after hydrothermal doping, and hence, the hydrogen storage capacities were improved. The hydrogen storage capacity of the N-doped ACs was 3.10 wt.% at 77 K and 1 bar, showing an enhancement factor of 1.13 and corresponding to the NAC with both highest surface area (3485 m2/g) and N content (2.2 wt.%). Statistical analysis showed that both the N content and surface area had positive contributions to the hydrogen storage, and it also could be predicted by the linear model from the N content and surface area. These results were among the best in hydrogen storage carbon materials, and the high hydrogen storage capacities were attributed to the high surface area.