Using the Integrated Terrestrial Ecosystem Carbon Cycle model (InTEC), six simulations with different input scenarios of climate, CO 2 , and nitrogen (N) deposition are conducted to study the changes of soil carbon (C) content in Canada's forests and wetlands during 1901–2000. Simulated total C stored in Canada's forest and wetland soils is 164.5 Pg C and accounts for about 7% of the global total of 2400 Pg C to the depth of 2 m, implying the significance of Canada's forest and wetland soils in the global terrestrial C cycle. Soils of Canadian forests and wetlands sequestrated 3.9 Pg C (2.6 Pg C in forests and 1.3 Pg C in wetlands) during 1901–2000 because of the integrated effects of climate, CO 2 fertilization, N deposition, and forest age factors. The changes of soil C content during 1901–2000 ranged spatially from −2 kg C m −2 to 4 kg C m −2 , depending on fire disturbance history, climate change pattern, and N deposition rates. Soil C increased by 2 to 4 kg C m −2 in Eastern Hudson Plains, Eastern Middle Boreal Shield, Southern Boreal Shield, and Atlantic Maritime and decreased by more than 1 kg C m −2 in Southern Boreal Plains. Simulations shows that climate influences growing conditions, growing season length, net N mineralization, and N fixation and therefore was the biggest driver of the increase in total soil C content during 1901–2000, followed by CO 2 fertilization and N deposition. The climate‐induced increase of soil C occurred mainly in the cool and wet period from the middle 1940s to the middle 1970s. Overall, an increase of 1°C in mean annual temperature induced heterotrophic respiration to increase by 62 Tg C a −1 . In contrast to the century‐scale trend from 1901 to 2000, during the last two decades (1981–2000), CO 2 fertilization was the biggest driver of the increase in soil C, while climate change alone caused soil C to decrease.