Three bis(6-amino-1,3-dimethyluracil-5-yl)-methane derivatives were studied experimentally by variable-temperature 1H NMR in polar aprotic solutions (CD2Cl2, C5D5N, C2D2Cl4) and computationally by DFT. The unusual for diarylmethanes coplanar conformation of dimethyluracil rings of each molecule is held by a pair of unequal intramolecular N-H⋯O hydrogen bonds. We show the presence of two dynamic processes involving breakage/formation of these bonds. First, it is two independent NH2 group rotations, each coupled to nitrogen inversion. Second, it is uracil ring rotations (ring flips). The thermodynamic parameters (ΔH‡, ΔS‡, and ΔG‡) of both processes were estimated by the full line shape analysis of NMR signals and also by DFT calculations. We demonstrate that, though the ring flips exchange pairs of NH protons, the two processes are not coupled: during the ring flip NH2 groups do not rotate, and during the NH2 rotation the rings do not necessarily rotate. Unlike in many other diarylmethanes, the ring flips in the studied compounds are happening stepwise; i.e., the configuration when both rings are "in flight" at the same time is energetically unfavorable (small degree of "cog wheel effect"). The signs of the ΔS‡ values indicate that the molecular flexibility increases during the NH2 rotations, but decreases during the ring flips.