Thin films provide a versatile platform to tune electron correlations and explore new physics in strongly correlated materials. Epitaxially grown thin films of the alkali-doped fulleride K$_{3+x}$C$_{60}$, for example, exhibit various intriguing phenomena, including Mott transitions and superconductivity, depending on dimensionality and doping. Surprisingly, in the trilayer case, a strong electron-hole doping asymmetry has been observed in the superconducting phase, which is absent in the three-dimensional bulk limit. Using density-functional theory plus dynamical mean-field theory, we show that this doping asymmetry results from a substantial charge reshuffling from the top layer to the middle layer. While the nominal filling per fullerene is close to $n=3$, the top layer rapidly switches to an $n=2$ insulating state upon hole doping, which explains the doping asymmetry of the superconducting gap. The interlayer charge transfer and layer-selective metal-insulator transition result from the interplay between crystal field splittings, strong Coulomb interactions, and an effectively negative Hund coupling. This peculiar charge reshuffling is absent in the monolayer system, which is an $n=3$ Mott insulator, as expected from the nominal filling.