Climate warming poses a severe threat to coral reefs, making it crucial to understand species-specific resilience mechanisms. We investigated thermal stress responses in two coral species, Porites lutea (massive) and Acropora acuminata (branching), collected from Pulau Payar Marine Park, Malaysia. Coral fragments were exposed to short-term elevated temperatures (32°C and 34°C) and then returned to ambient conditions (30°C) to evaluate recovery. We measured reactive oxygen species (ROS) production, chlorophyll a content, symbiont density, lipid reserves, and photosynthetic performance (Fv/Fm) as indicators of physiological stress and resilience. Results revealed pronounced interspecific differences. At 34°C, A. acuminata exhibited acute stress: high ROS levels, significant declines in chlorophyll-a and symbiont density (bleaching), and a sharp drop in Fv/Fm. In contrast, P. lutea showed more moderate responses, retaining higher symbiont densities and photosynthetic efficiency. Both species tolerated 32°C better, but A. acuminata still showed earlier signs of stress than P. lutea. Upon return to 30°C, P. lutea demonstrated rapid, near-complete recovery of Fv/Fm and symbiont populations, whereas A. acuminata’s recovery was slower and incomplete. Notably, P. lutea maintained its lipid reserves, while A. acuminata depleted its lipid stores to sustain metabolism. Coupled with P. lutea’s stronger antioxidant capacity, these factors likely mitigated oxidative damage in P. lutea and underlie its superior performance. These findings highlight distinct thermal tolerance thresholds, with the massive P. lutea exhibiting greater resilience than the branching A. acuminata. Understanding such species-specific responses is critical for coral reef conservation in a warming world. Our results suggest that management strategies should incorporate species-specific tolerance levels – for instance, prioritizing resilient corals and mitigating stressors for vulnerable species to foster climate-resilient coral reefs.