Oxidative stress (OS) and fluctuating asymmetry (FA) as risk markers for environmental stress are widely used to predict changes in the health and fitness of many animals exposed to pollutants. However, from the perspective of protecting declining amphibians, it remains to be verified which one would be a reliable indicator for amphibians exposed to long-term heavy metal pollution under natural conditions. In this study, the OS and FA of Bufo raddei exposed to natural heavy metal pollution were analyzed to determine which marker is more accurate for indicating heavy metal-induced stress. Three years of data were collected during the breeding season of B. raddei from Baiyin (BY), which has been mainly contaminated with Cu, Zn, Pb, and Cd compounds for a long period, and from Liujiaxia (LJX), which is a relatively unpolluted area. Unexpectedly, although significant accumulation of the four heavy metals was found in the kidney and liver of B. raddei from BY, the levels of superoxide dismutase, glutathione peroxidase, and malondialdehyde in these two organs were found to be irregular, with low repeatability in both BY and LJX. However, significant differences in the levels of FA were observed in B. raddei populations from these two areas over the past 3 years (P < 0.01). The degrees of FA in B. raddei populations from BY and LJX were assessed as degree 4 and 1, respectively. In short, this study suggested that FA was a more reliable and effective indicator than OS to monitor and predict long-term environmental stress on anuran amphibians.