Despite growing concerns over mercury (Hg) accumulation in birds in recent decades, little is known about Hg exposure in nocturnal migratory birds. Here, total mercury (THg) and methylmercury (MeHg) were detected in the feathers of nocturnal migratory birds (n = 286, belonging to 46 species) passing through Mount Ailao in Southwest China. The stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) were also determined to clarify the effects of trophic position, foraging guild, and foraging behavior on Hg bioaccumulation. Our results show that the THg and MeHg concentrations varied by two orders of magnitude among all nocturnal migratory birds investigated, with the lowest values (THg: 0.056 mg kg− 1 ; MeHg: 0.038 mg kg− 1 ) in the Asian koel (Eudynamys scolopaceus) and the highest (THg: 12 mg kg− 1 ; MeHg: 7.8 mg kg− 1 ) in the hair-crested drongo (Dicrurus hottentottus). Waterbirds showed higher δ15N values and higher THg and MeHg concentrations than songbirds, and the Hg concentrations in piscivorous species were significantly higher than those in herbivores, omnivores, and insectivores. Significant effects of foraging guilds (Kruskal–Wallis one-way ANOVA, p < 0.001) and foraging behaviors (Kruskal–Wallis one-way ANOVA, p < 0.001) on the Hg concentrations in migratory bird feathers were detected. A risk assessment indicated that approximately 7.0% of individuals were at moderate (2.4–5.0 mg kg− 1 ) to high (>5.0 mg kg− 1 ) risk of Hg exposure, and were therefore vulnerable to adverse physiological and behavioral effects. A long-term monitoring campaign during the migratory period is highly recommended to better understand the bioaccumulation of Hg in these nocturnal migratory bird populations over time.