With the popularization of carbon and nitrogen stable-isotope analysis methods used on archaeological samples from Xinjiang, the ancient paleodiet there has been revealed. However, research about isotopic analysis combined with environmental factors is rare, especially in such a variable and complex climate as that of the Tianshan region. We systematically analyzed the δ13C and δ15N results from animals and humans for dietary reconstruction of nomadic pastoralists from the Tianshan region during 3900–1200 cal BP. The δ13C and δ15N values for animals (sheep/goat, horse and cattle; n = 57) have a wide range from –20.8‰ to –14.7‰ for δ13C (–19.2 ± 1.0‰) and 3.2‰ to 9.9‰ for δ15N (7.0 ± 1.2‰). The δ13C and δ15N values from humans range from –19.6 to –12.3‰ (–16.0 ± 1.5‰) and 7.1 to 16.7‰ (–13.6 ± 1.5‰), respectively. The animal δ15N results indicate that the dry environment in the Tianshan region may result in elevated δ15N values. Synthesizing animal and human isotope results suggests that the inhabitants engaged in mobile herding economies subsidized with crops and wild animal meat from the Tianshan Mountains. In conclusion, we found that the regional environment closely relates to crop types, and temporal climate change has an effect on human dietary structure. Therefore, climate condition cannot be ignored when studying human paleodiet.