Compound drought and heat events (CDHEs) and forest cover change influence regional forest carbon dynamics. Changes in regional vegetation biomass and soil carbon storage induced by forest cover change often exhibit considerable uncertainty, and previous research on the impacts of CDHEs on forest carbon dynamics is limited. To accurately quantify the specific effects of forest cover change and CDHEs on forest carbon dynamics in different regions, we employed a combined algorithm of the Carnegie–Ames–Stanford Approach (CASA) and bookkeeping empirical models to examine the impact of regional forest cover changes on forest carbon dynamics during 2000–2022 in Nanjing and Shaoguan, Southern China. Using the Geographical Detector model, we then analyzed the effects of CDHEs on forest carbon dynamics. Next, we used the photosynthesis equation and the optimal response time of forests to drought (heat) events to calculate the changes in forest carbon sequestration caused by CDHEs in both regions during 2000–2022. The results indicated that afforestation and deforestation led to +0.269 TgC and +1.509 TgC of carbon sequestration and 0.491 TgC and 2.802 TgC of carbon emissions in Nanjing and Shaoguan, respectively. The overall effects of CDHEs on the change in forest carbon sequestration were manifested as net carbon loss. In Nanjing, the net carbon loss caused by CDHEs (0.186 TgC) was lower than the loss due to forest cover change (0.222 TgC). In Shaoguan, the net forest carbon loss caused by CDHEs (3.219 TgC) was much more significant than that caused by forest cover change (1.293 TgC). This study demonstrated that forest carbon dynamics are dominated by different factors in different regions, which provides a scientific basis for local governments to formulate targeted forest management policies.