The stocks and distribution of soil carbon and soil nitrogen have been affected by disturbance of natural and artificial disturbance in the Three Gorges Reservoir region. China fir and Masson pine mixed forest is the most widely distributed vegetation type in the area but much natural vegetation has been changed, with the zonal vegetation replaced by natural or artificial coniferous forests, shrubs and shrub-herbs, and even bare land, resulting in ecosystem degradation. This study assessed spatial variability and seasonal changes in soil carbon and nitrogen in this region under different disturbed conditions. In autumn 2008 and spring 2009, soil samples were collected to a depth of 20 cm using a 3.0 m × 3.0 m grid in 900m² (30.0 m × 30.0 m) plots in areas of different disturbance. Samples were collected from 294 sampling points to study the spatial variability and seasonal changes in soil carbon and nitrogen using geostatistics. Significant differences in soil nitrogen concentrations were found between seasons, and in soil carbon concentrations only following serious disturbance (P <0.05). The degree of disturbance had a significant effect on soil carbon and nitrogen concentrations in autumn (P <0.05), and both soil carbon and nitrogen concentrations were significantly correlated with soil moisture and pH (P <0.01). Acidic soil pH values between 4.59 and 5.15 contributed to soil carbon and soil nitrogen sequestration and accumulation in the area. The soil carbon to nitrogen ratio was related to the degree of soil mineralization and human disturbance The spatial autocorrelation between soil carbon and nitrogen was weakened by intensive human disturbance and condition of the earth’s surface status. The geostatistical analysis indicated that the semivariance graphs were expressed by the spherical model in areas with no human disturbance, and that there were significant differences in the spatial autocorrelation ranges between seasons, with the effective range (a)of soil carbon being 61.90 m in autumn and 60.96 m in spring, and of soil nitrogen being 62.38 m in autumn and 61.52 m in spring. In disturbed areas, the spatial distribution characteristic was not obviously reflected by the semivariance graphs, and the effective range changed somewhat. Concentrations of soil carbon and soil nitrogen were related to soil moisture, pH values, seasons and disturbance factors. Spatial variability in soil carbon and nitrogen in the region was mostly contributed by the influencing factors including the age of the China fir and Masson pine mixed forest, extent of shrub cover, slope and human disturbance.