Patterned polymer films are known to exhibit shape evolution when annealed at temperatures close to or above the glass transition temperature. Here, we employ small-angle X-ray scattering to address the size-dependent shape evolution of poly(methyl methacrylate) (PMMA) gratings obtained by thermal nanoimprint lithography. Using an iterative phase-retrieval scheme, we reconstruct the height profile of the grating in situ in a model-independent manner during a heating ramp through the glass transition. This allows us to directly observe the evolution from a trapezoidal shape, via a sinusoidal-like one, into a flat film, in agreement with ex-situ atomic force microscopy experiments. Moreover, we find the onset temperature of shape evolution to decrease monotonically with decreasing pattern size, the difference being similar to 4 degrees C between gratings with periods of 240 and 80 nm. We primarily attribute the size-dependent shape evolution to a reduction in viscosity with decreasing pattern size, which is induced by either free-surface effects or surface-tension-driven non-Newtonian flow.