<p>Frequent droughts pose considerable threat to global forest carbon uptake, but little is known about the response of forest carbon fluxes in climatic transition zones to seasonal drought. In this study, the responses of carbon fluxes to seasonal drought in two natural forests (<i>Quercus aliena var. acute serrata Maxim</i> and <i>Pinus tabuliformis Carr.</i>) in the Baotianman Nature Reserve were investigated. The <i>Q. aliena</i> forest exhibited a high resilience with stable gross primary productivity (<i>GPP</i>). However, ecosystem respiration (<i>Re</i>) significantly declined by 18.4% compared with normal years, leading to an increase in net carbon sequestration capacity of 4.1%. This resilience was attributed to its deep root system accessing soil water (<i>SWC</i>_50cm) to sustain stomatal openness, coupled with the efficient utilization of photosynthetically active radiation to drive photosynthesis. In contrast, the <i>P. tabuliformis</i> forest, which relied on shallow soil moisture (<i>SWC</i>_20cm), experienced simultaneous decreases in both <i>GPP</i> and <i>Re</i> during drought, with a sharply greater decrease in <i>GPP</i>, resulting in low net carbon sink capacity. Further analysis revealed that the <i>Q. aliena</i> forest prioritized carbon assimilation through a deep water-stomatal synergy strategy (anisohydric behavior), whereas the <i>P. tabuliformis</i> forest adopted an isohydric strategy favoring water conservation at the expense of carbon fixation efficiency. These findings highlight distinct mechanisms underlying drought adaptation between forest types, providing critical insight into optimizing forest carbon cycle models and selecting drought-resistant species under the influence of climate change.</p>