The marginal areas of the Tibetan Plateau have great vertical altitude gradient and abundant vegetation, they are therefore the ideal places for investigating the relationships among carbon isotope composition (δ13C) of modern soils, vegetation and environmental factors, which would be very useful for the reconstructions of both paleovegetation and paleoclimate. In this paper, modern soil samples collected in different vegetation vertical zones along 4 km elevation gradient in the eastern margin of the Tibetan Plateau were analyzed for their carbon isotope composition. The results show that the modern soils in different vegetation vertical zones show apparent difference of δ13C values, which get heavier in the sequence of mixed evergreen and deciduous broad-leaved forest (−27.28‰ on average), evergreen broad-leaved forest (−27.25‰), subalpine shrub-meadow (−25.81‰), subalpine coniferous forest (−25.81‰), alpine bush-meadow (−25.16‰), and drought-enduring shrub (−24.07‰). 1800 m and 3500 m are two critical points for the δ13C values with respect to altitude. Specifically, the δ13C values decrease with increasing altitude below both points while increasing with increasing altitude above both points. Further analyses indicate that the declining δ13C values are mainly controlled by the decreasing proportion of C4 plants with elevation and the increasing δ13C values are attributed to the plant physic-morphological adaptation to the alpine environment. In the absence of drought stress, temperature is the main controlling factor for the carbon isotopic variations with altitude gradient.