Forest management is one of the important nature-based solutions for climate mitigation. Thinning can indirectly influence tree physiology by changing the microclimate and directly change the stand biomass, which can impact forest carbon sequestration. However, previous results about how thinning might influence carbon stocks remain inconsistent regarding post-thinning carbon accretion. In this study, crop tree release (CTR) thinning in four intensities (CK: 0% of basal area removal, LT: 17.25%, MT: 34.73%, and HT: 51.87%) were conducted in a temperate deciduous forest in Jiaohe, northeastern China in 2011. Plot inventories in 2011, 2013, 2015, 2018 and 2021 and tree cores collected in 2017 and 2018 offered the opportunity to examine how are the interannual carbon sequestration ability of Korean pine and Manchurian ash responded to CTR thinning in four intensities. We quantify the carbon sequestration ability of trees by calculating individual stem carbon stock and annual carbon stock rate to examine whether the previous inconsistency was attributed to different responses of species, and the ignorance of frozen carbon content. The results show: (1) after thinning, the underestimation of carbon stocks of Manchurian ash decreased with the increasing thinning intensity. The greatest underestimation of Manchurian ash reaches 2922 kg ha−1, while that of Korean pine only reaches 283 kg ha−1. Compared with Manchurian ash, the conventional carbon fraction of 0.5 for Korean pine is more appropriate, and the misestimation of Korean pine didn't show an obvious pattern with the intensity of thinning. (2) Under light thinning, both species maintained a stable carbon stock growth, and the frozen carbon content of Korean pine was significantly increased. During the 10 years after light thinning, the individual stem carbon of Korean pine increased from 57 kg to 81 kg, and Manchurian ash increased from 201 kg to 268 kg. The average rate of increase of individual stem carbon is positively related to tree size. Removing such large-diameter trees from the stand is likely to decrease carbon stock rate. Therefore, it is essential to design carbon-friendly silviculture prescriptions worldwide under the consideration of species, sizes, and intensities.