As an archetypal antiperovskite nitride compound, GeNCr3 undergoes a temperature-driven first-order antiferromagnetic-paramagnetic transition at approximately 418 K, accompanied with a structural phase transition from space group P-421m to I4/mcm. In this paper, we show that the critical temperature of GeNCr3 can be tuned from 418 to 240 K by doping manganese ions. Simultaneously, the evolution of the magnetic transition is consistent with the structural transition. Using temperature-dependent X-ray diffraction and X-ray photoelectron spectroscopy, in combination with first-principles calculations, we demonstrate that doping manganese ions tend to occupy the equatorial plane of the nitrogen octahedron. •The magnetic transition accompanied by a structural transition in GeNCr3 can be significantly shifted from 418 to 240 K by doping Mn ions.•The position of doping Mn is accurately identified at the atomic level by DFT.•The physical mechanism is discussed and analyzed from the perspective of crystal structure.