Corals' regulation of internal calcifying fluid (CF or cf) chemistry is crucial for their extraordinary calcification capacity, endowing them with a certain ability to cope with environmental changes such as anthropogenic ocean acidification (OA) and warming. However, it remains unclear whether the impacts of these changes on corals have substantially surpassed their regulation capacity, particularly in comparison to the CF chemistry responses to natural climate variability with minor or no human perturbation. In this study, we reconstructed the pH, dissolved inorganic carbon, and carbonate ion concentrations in coral CF (pHcf, DICcf, and [CO32−]cf) during the Mid- to Late-Holocene, by analyzing the skeletal δ11B and B/Ca of 80 Porites spp. from eastern Hainan Island in the South China Sea (SCS). Our records indicate considerable inter-colony variations in CF chemistry, with maximum disparities reaching 0.18 units for pHcf and 1664 μmol/kg for DICcf. With this in mind, we found no clear responses of coral DICcf to the climate fluctuations during the past ∼5500 years, nor evident differences in pHcf and [CO32−]cf across pre-industrial natural epochs. However, pHcf and [CO32−]cf of modern corals have significantly declined compared to fossil corals. Further analyzes compiling global data on Porites spp. also confirm this pronounced pHcf decrease in modern corals, suggesting the limitations of pantropical corals to counteract OA by up-regulating pHcf. Importantly, these fossil and modern corals reveal a clear long-term pHcf descending trend parallel to atmospheric CO2 changes, supporting the reliability of coral δ11B in recording long-term changes in seawater pH (pHsw).