Valence electron concentration (e/a) dependence of phase transition temperature TM, i.e., a higher e/a leading to an elevated TM, is a well-accepted criterion for the Ni–Mn-based alloys. However, this tendency is not always obeyed by certain alloy systems, such as the Ni2Mn(Ga, Z) alloys (Z = Si, Ge, and Sn). The origin of this abnormal behavior remains uncovered. In this work, by first-principles calculations, the origin of the abnormal e/a dependence of phase stability in the Ni2MnGa1−xSix (x = 0–1) alloys is elucidated through examining the electronic structure, phonon, and magnetism. We find that the abnormal e/a dependence of phase stability intrinsically originated from the chemical composition change. The composition variation brings about a reduction of the minority-spin electronic states near the Fermi energy and the weakness of the Fermi surface nesting. Moreover, the substitution of Si for Ga leads to a decreased magnetization of austenite and an increased magnetization of martensite, which also makes a non-negligible contribution to the abnormal phase stability. The conclusions drawn for the Ni2MnGa1−xSix alloys can be well extended to understand the structural transition in other abnormal alloying systems, such as the Ni2MnGa1−xZx alloys (Z = Ge and Sn). This work clarifies the origin of the abnormal dependence of phase stability on e/a in the Ni–Mn-based alloys and provides solid knowledge for the design of advanced magnetic shape memory alloys. ACKNOWLEDGMENTS