Pyrimidine derivatives have important applications in the fields of medicine, chemical industry and functional materials. In drug discovery, especially in the research and development of anticancer drugs, 5-bromo-2-(4-methylpiperidin-1-yl)pyrimidine is a significant intermediate containing a pyrimidine ring. In this paper, 5-bromo-2-(4-methylpiperidin-1-yl)pyrimidine was prepared by one-step aromatic nucleophilic substitution reaction, and its single crystal was obtained by solution crystallization, and crystallographic analysis was carried out (crystal system: orthorhombic, space group: P212121, unit cell: a=10.181 42(6) nm, b=17.620 0(8) nm, c=10.179 02(5) nm, Z=4, ρc=1.478 g·cm-3, R=0.056 6, wR=0.168 8). By the way, the crystal structure shows that the intramolecular hydrogen bonds and the van der Waals forces jointly maintain the stable arrangement of molecules space, and hydrogen bonds are one of the key factors for crystal stability. In B3LYP/6-311G(d, p) mode, density functional theory (DFT) was used to calculate the optimal structure and frontier orbit energy, and the result of DFT optimization is similar to the experimentally determined data. The structure and the results are basically the same. In addition, in order to further reveal the physicochemical properties of the title compound, the molecular electrostatic formula and frontier molecular orbital were further investigated by DFT.