Global warming has a significant impact on soil carbon dioxide (CO2) and methane (CH4) fluxes in temperate forests. However, due to a lack of field observations, limited information is available about the responses of soil CO2 and CH4 fluxes to changes in temperature during the non-growing season and throughout the year in temperate forests. The broadleaf and Korean pine mixed mature forest (MF) and adjacent secondary white birch forest (BF) at different succession stages in the Changbai mountain region in northeastern China were selected, to study the effect of in situ soil column translocation on CO2 and CH4 fluxes in temperate forests. On average, the air temperature and soil temperature at 5 cm depth under BF stands from October 2018 to October 2022 increased by 0.64 and 0.42 °C during the non-growing season and by 0.49 and 0.43 °C throughout the year, respectively, compared with those under MF stands. Based on multi-year measurements in field experiments, it was shown that during the non-growing season, fluxes of CO2 and CH4 from soil columns under MF and BF stands ranged from 0.004 to 1.175 and from 0.015 to 1.401 (averages of 0.321 and 0.387) μmol CO2 m−2 s−1, and from −1.003 to 0.048 and from −1.037 to −0.013 (averages of −0.179 and −0.250) nmol CH4 m−2 s−1, respectively, accounting for approximately 20.8% and 25.3%, and 48.8% and 69.1% of the corresponding average fluxes during the growing season. When undisturbed soil columns of MF were transferred to a BF stand, to simulate warming, the cumulative soil CO2 emissions and CH4 uptake increased by 23.5% and 15.3% during the non-growing season, and by 9.5% and 16.3% across the year, respectively. However, when soil columns of BF were transferred to a MF stand, to simulate cooling, the cumulative soil CO2 emissions decreased by 16.9% and 0.1% during the non-growing season and across the year, respectively. Upon cooling, the cumulative soil CH4 uptake decreased by 21.8% during the non-growing season but increased by 15.4% across the year. The soil temperature and moisture at 5 cm depth in soil columns could explain 84–86% of the variability in CO2 fluxes and 16–51% of the variability in CH4 fluxes under the two forest stands throughout the field measurement period. The results of the in situ soil column translocation experiments highlight that a small climate warming in nature can increase soil CO2 emissions and CH4 uptake in the temperate forests of northeastern China, particularly during the non-growing season, which should be considered when predicting soil C fluxes in the temperate forests of northeastern China under global warming scenarios.