Although variant selection during the phase transformation of zirconium (Zr) alloys has been studied extensively, studies on the formation mechanism of microstructural characteristics related to α variant selection remain limited. The formation mechanisms of the self-accommodation morphology and inter-variant boundary characteristics of α variants in homogenized Zr–2.5Nb alloy cooled by water quenching (WQ), furnace cooling (FC), and air cooling (AC) were systematically investigated from the perspective of local strain during phase transformation. The α variants exhibited triangular morphologies in both the WQ and AC samples, and a colony morphology in the FC sample. Further, there were five types of inter-variant boundaries: Type I <0 0 0 1>/10.53°, Type II < 1 1 2 ‾ 0 > /60°, Type III < 1.377 ‾ 1 ‾ 2.377 0.359 > /60.83°, Type IV < 10 ‾ 5 5 3 ‾ > /63.26°, and Type V < 1 2.38 ‾ 1.38 0 > /90°. The proportion of Type II is up to 98 % in the AC sample and 57.9 % in the WQ sample; the Type I was very low in all three samples; and a high proportion of the Type V was observed in the FC sample (23.6 %). The self-accommodation morphology of α variants is closely related to the equivalent strain ( ε VM ) during the variant selection. Theoretical calculations indicated that, for a specific 2-variant combinations, there were always one or more 3-variant combinations with a lower ε VM than the 2-variant combinations. A lower ε VM contributes to the presence of 3-variant combinations, which forms a triangle morphology. The formation of inter-variant boundaries is determined by the type and frequency of variants as well as the ε VM of the 2-variant combinations. The order of the mean values of ε VM for the five types of boundaries was Type II (0.0757), Type III (0.0859), Type IV (0.1012), Type V (0.1112), and Type I (0.1307). That is, Type II is the easiest and Type I is the most difficult, which resulted in a very high fraction of Type II and a very low fraction of Type I in the WQ, AC, and FC samples. The presence of a high fraction of Type V in the FC sample was related to the type and fraction of each variant.