The topological effects of phonons are extensively studied in various materials, which have the potential to improve heat dissipation in power electronics due to its intrinsic, topologically protected, nondissipative phonon surface states. Nevertheless, the phase transition of the Weyl phonons in nitrides is yet to be elucidated. To unveil the microscale origin, topological phonon properties in AlGaN alloys are investigated from first principles. It is found that phase transitions in Weyl phonons are evidently present in AlGaN alloys and nitride single crystals. Under strain states, both GaN and AlN show a more prominent phase transition of Weyl phonons when subjected to biaxial compressive and uniaxial tensile strains. It has been observed that the zz components in the self‐term and the transverse first‐nearest‐neighbor (1NN) force constants (FCs) are the most influential. The noncontinuous Weyl phonon phase transition in AlGaN alloys is reflected in the normalized self‐term and 1NN FCs, which vary in a nonlinear fashion with increasing magnitude. With increased branches in AlGaN alloys, hundreds of Weyl phonons are present accompanied by significant disorders in normalized FCs, which mainly occur for N atoms in self‐terms and for all components in normalized 1NN FCs.