This paper is concerned with a singular limit of the Kobayashi–Warren–Carter system, a phase field system modelling the evolutions of structures of grains. Under a suitable scaling, the limit system is formally derived when the interface thickness parameter tends to zero. Different from many other problems, it turns out that the limit system is a system involving fractional time derivatives, although the original system is a simple gradient flow. A rigorous derivation is given when the problem is reduced to a gradient flow of a single-well Modica–Mortola functional in a one-dimensional setting.