The embankment section dimension affects heat exchange area on embankment surface and the heat transfer condition of embankment, and thus affect the water, heat and deformation characteristics of embankment in permafrost regions. In this study, based on the theories of heat transfer, frozen soil mechanics and frozen soil physics, a mathematical model of water-heat transfer and coupling deformation for embankment is deduced to analyze the influence of embankment section dimension on its water, heat and deformation characteristics. The calculation results show that widening embankment causes the heat accumulation effect in the middle of embankment, which affects the thawing depth, warming rate and thawing rate of permafrost, and increases the unfrozen water content, displacement and thawing period of underlying soil. The extension of the thawing period shortens the freezing period, resulting in the reduced frost heave deformation, which is offset by creep deformation over time. Increasing embankment height can reduce the thawing depth, warming rate and thawing rate of permafrost, but can promote the formation of residual thawed layer. The frost heave hardly occurs after the residual thawing layer is formed, resulting in less frost heave deformation on embankment surface.