In this work, SnO2 nanoflowers synthesized by a hydrothermal method were employed as hydrogen sensing materials. The as-synthesized SnO2 nanoflowers consisted of cuboid-like SnO2 nanorods with tetragonal structures. A great increase in the relative content of surface-adsorbed oxygen was observed after the vacuum annealing treatment, and this increase could have been due to the increase in surface oxygen vacancies serving as preferential adsorption sites for oxygen species. Annealing treatment resulted in an 8% increase in the specific surface area of the samples. Moreover, the conductivity of the sensors decreased after the annealing treatment, which should be attributed to the increase in electron scattering around the defects and the compensated donor behavior of the oxygen vacancies due to the surface oxygen adsorption. The hydrogen sensors of the annealed samples, compared to those of the unannealed samples, exhibited a much higher sensitivity and faster response rate. The sensor response factor and response rate increased from 27.1% to 80.2% and 0.34%/s to 1.15%/s, respectively. This remarkable enhancement in sensing performance induced by the annealing treatment could be attributed to the larger specific surface areas and higher amount of surface-adsorbed oxygen, which provides a greater reaction space for hydrogen. Moreover, the sensors with annealed SnO2 nanoflowers also exhibited high selectivity towards hydrogen against CH4, CO, and ethanol.