Stable isotopic (C, O) analysis of fossil enamel bioapatite has been widely used in paleontological fields to reconstruct the paleoecology and paleoenvironment. It is common to compare the isotopic data of enamel bioapatite made by different pretreatment and measuring methods in different labs, without considering the isotopic variations possibly caused by different protocols. Here, we chose the same samples from Gigantopithecus fauna in the Longgu Cave (Longgudong), Hubei and remeasured their δ¹³C and δ¹⁸O values, which had been previously reported in Zhao et al. (2011) and Nelson (2014) with different pretreatment and measuring methods, in order to evaluate the effects of the above factors on the isotopic variability. The comparison among three isotopic dataset indicates that there did exist small isotopic variations on the δ ¹³C and δ ¹⁸O values. It seems that the δ ¹³C values were more influenced, probably due to differential practices to eliminate the diagenetic effects using varied chemicals and retaining reaction time during the process of bioapatite preparation. However, we should emphasize that the small isotopic variations observed here do not have produced substantial isotopic variance among fossil taxa and localities, providing the preliminarily theoretical foundation to make isotopic comparison directly. Even so, we still recommend that it is best to compare the isotopic data according to the same preparing and measuring protocols to remove the systematic errors or to re-measure samples again in different labs to calibrate the data.