The interplay between magnetic, megneto-transport and structural properties of Nd-doped double perovskite Sr2−xNdxFe1+yMo1−yO6, in the range 0.05 < x < 0.45 for y = x/2 and synthesized by solid state reaction, has been investigated. Specifically, it has been shown that the observed tetragonal to monoclinic crystallographic phase transition at the Nd composition in the range x = 0.10 to x = 0.15 is in close relationship with its magnetic and magnetoresistive behavior. The observed crystallographic transition, confirmed by X-ray diffraction experiments, is consistent with the decrease of the unit cell volume when the Nd doping content increases. Besides, the Curie temperature determined by thermogravimetric experiments increases with the Nd content just after the structural transition. Furthermore, the increase of Nd doping up to x = 0.45 in the double perovskite structure leads to a magnetization loss about 98% as a result of the increase of both, anti-site defects and the number of charge carriers. The progressive magnetization loss with Nd doping is also responsible for the observed monotonic decrease of the magnetoresistance ratio due to the predominance of the antiferromagnetic order. Particularly, the electrical behavior in the vicinity of the crystallographic transition is characterized by a very slight increase followed by a rapid drop of the magnetoresistance ratio, which is originated by the corresponding fluctuations of the saturation magnetization.