Diverse, multi-stage phase transformations occur in many materials under extreme environments. In response to irradiation, some MAX phase compositions transform from an initial hexagonal structure to an intermediate γ-phase, then to a face-centered cubic (fcc) structure, while others instead become amorphous. To date, no comprehensive description of the associated transformation mechanisms, or of the influence of composition on this phase behavior, has been reported. In this work, we combine in situ ion irradiation, Transmission electron microscopy (TEM), and density-functional theory (DFT) calculations to demonstrate the distinct transformation pathways and corresponding energetics of the γ-to-fcc transformation in a series of MAX phases. We show that structural distortion and bond covalency of the intermediate γ-phase determine the outcome of the transformation process. This yields a generalized rule to predict the phase transition behaviors of MAX phases based on their atomic radii and electronegativity. These results provide an insight into the multi-stage phase transformation pathways along which MAX phase systems and related complex materials evolve in extreme environments. Researchers present the evidence and mechanism of distinct phase transformation pathways in MAX phases under ion irradiation, providing a new theory and predictive method for phase behavior based on composition, advancing understanding of materials in extreme conditions.