A structural phase transition of an intercalation compound Mn1/4NbS2 has been investigated by X-ray diffraction at high temperatures. The lattice parameter c exhibited a discontinuous change at 640K. The superlattice reflections observed below 640K disappeared suddenly above 640K. The phase transition at 640K took an aspect of the first-order phase transition. The precise structure analyses were performed at various temperatures above and below the phase-transition temperature. It was revealed that Mn atoms were arranged in disorder in the high-temperature phase, while the Mn atoms were ordered forming the 2a(0) x 2a(0) x c(0) superlattice in the low-temperature phase. The Nh and S atoms around the ordered Mn atoms slightly shifted from the high-symmetry position in the low-temperature phase. The order parameters were the degree of order of the Mn atoms and the degree of displacement of the Nb and S atoms.