With climate change, frequent forest fires and prolonged fire period occur all over the world. Moreover, carbon emission from forest fire affects the carbon cycle of the forest ecosystem. However, this effect varies by region with no uniform conclusions, and fewer comparative studies exist on such differences between regions. In this paper, net primary productivity (NPP) data MOD17A3 were used as an important parameter of forest carbon absorption, along with MODIS fire spot data MCD14DL and burned area data MCD64A1. Forest carbon lost under forest fire interference in the northeast and southwest natural forest areas of China was studied to explore the role of forest fire in the carbon cycle process and its differences in the unlike regions of China. Here, by means of kernel density analysis and M-K trend test, the characteristics of forest fires in China’s southwest and northeast forests were calculated. Forest carbon emission under forest fire disturbance was quantified by reference to the forest fire emission factor list. We show that (1) the total number of forest fire spots in the southwest region from 2001 to 2020 was 1.06 × 105, 1.28 times that of Northeast China. However, the total burned area in the southwest was only 67.84% of that in the northeast. (2) The total carbon emissions from forest fires in the southwest from 2001 to 2020 was 37,559.94 Gg, 10.77% larger than the northeast forest, CH4 and CO2 were 13.52% and 11.29% larger respectively. Moreover, the carbon emissions of forest fire in the northeast showed a downward trend, R2 = 0.16 (p < 0.1), while it remained basically unchanged in the southwest. The contribution of carbon emissions from forest fires changed with forest types, it was shown as: evergreen needleleaf forest (14.98%) > evergreen broadleaf forest (10.81%) > deciduous needleleaf forest (6.52%) > deciduous broadleaf forest (5.22%). (3) From 2001 to 2020, under the premise that the NPP both manifested upward trends, the NPP of the burned areas showed a significant downward trend in the southwest forest, with R2 = 0.42 (p < 0.05), while it increased in the northeast forest, with R2 = 0.37 (p < 0.05). It showed negative correlation between NPP of burned areas and forest fire carbon emissions, and forest fire disturbance had no significant effect on forest NPP in Northeast China, while net carbon loss occurred in Southwest China. In general, under different forest fire characteristics, NPP, which represents forest carbon uptake, and carbon emissions from forest fires show differences. The impact of forest fire disturbance on forest carbon process varies with regions. The study can provide some ideas on the effects of forest fire disturbance on climate change.