An interesting anomaly of the diffusion process with an apparently negative diffusion coefficient defined through the mean-square displacement in a one-dimensional quantum molecular chain model is shown. Nevertheless, the system satisfies the H-theorem, so that the second law of thermodynamics is satisfied. The reason why the “diffusion constant” becomes negative is due to the effect of the phase mixing process, which is a characteristic result of the one-dimensionality of the system. We illustrate the situation where this negative “diffusion constant” appears.