High-value yak meat from Qinghai-Tibet Plateau was investigated using stable isotopes (δC, δH, δO, δN and δS) to identify attributes which could verify and protect its geographical origin. Supervised PLS-DA was applied to the isotope data to discriminate four geographical locations. δC, δH, and δO values showed significant differences according to origin while δN and δS values did not show any change across the different regions. Isotope values of different body tissues from the same animal showed no statistical difference for the five stable isotopes. In addition, the δH and δO values of defatted yak meat was highly correlated to farm altitude and associated drinking water. This yak meat traceability method is particularly useful to protect the Product of Geographical Indication (PGI) status of Gannan yak meat and verify the farming origin of yak meat sold in markets for food safety purposes, especially when excessive hormones, pesticides or heavy metals are found.