The excellent optoelectronic properties of metal halide perovskites (MHPs) have attracted extensive scientific interest and boosted their application in optoelectronic devices. Despite their attractive optoelectronic properties, their poor stability under ambient conditions remains the major challenge, hindering their large-scale practical applications. In particular, some MHPs undergo spontaneous phase transitions from perovskites to nonperovskites. Compositional engineering via mixing cations or anions has been widely reported to be effective in suppressing such unwanted phase transitions. However, the atomistic and electronic origins of the stabilization effect remain unexplored. Here, by using density functional theory calculations, we provide insights for the undesired phase transition of pristine perovskites (FAPbI3, CsPbI3, and CsSnI3) and reveal the mechanisms of the improved phase stability of the mixed compounds [CsxFA1–xPbI3, CsSnyPb1–yI3, and CsSn(BrzI1–z)3]. We identify that the phase transition is correlated with the relative strength of the M–X bonds as well as that of the hydrogen bonds (for hybrid compositions) in perovskite and nonperovskite phases. The phase transition can be suppressed by mixing ions, giving rise to either an increased bond strength for the perovskite or a decreased bond strength in their nonperovskite counterparts, or suppressed vacancy defect formation for Sn–Pb mixed perovskites. Our results present a comprehensive understanding of the mechanisms for the phase instability of MHPs and provide design rules for engineering phase-stable perovskite compositions.