(R,Zr)(Fe,Co)12−xTix (R = Nd and Sm) alloys of ten different compositions were prepared by strip-casting. The elemental distribution of the sample particles after annealing was quite homogeneous. Existing phases in the prepared alloys were determined by X-ray diffraction and the occupation sites of the substituted elements (Ti, Co, and Zr) were determined using spherical aberration corrected scanning transmission electron microscopy. The ThMn12 structure is stable in Ti1.0 compounds for both R = Nd and Sm, but exhibited obvious precipitation of α-(Fe,Co) phases in low Ti content compounds with Ti0.5. Ti substitution into Fe(8i) sites is important for the stabilization of the ThMn12 structure. Furthermore, the stability of low Ti content compounds could be recovered by the substitution of Zr into R(2a) sites. Co was mainly in Fe(8j) and Fe(8f) sites, which contributed to the stability of the 1–12 structure by increasing the configuration entropy. Analysis based on three Fe hexagons and two local sub-structural units suggested that the stabilization of ThMn12 structure by Ti and Zr substitutions mainly originates by resolving local mismatches in interatomic distances in the structure.