The high density of two‐dimensional electron gas (2DEG) in InAlN/AlN/GaN heterostructures results in significant occupation of higher subbands, it is thus imperative to consider multi‐subband occupation and inter‐subband scattering in the calculations of polar optical phonon (POP) scattering. The physical parameters, such as subband energies, wave functions of the four lowest subbands, and Fermi level of InAlN/AlN/GaN heterostructures, are calculated by solving the Schrödinger‐Poisson equations and applied to the multi‐subband POP scattering model. The dependence of mobility, which is limited by multi‐subband POP scattering, on temperature and 2DEG density is studied. The results show that multi‐subband occupation and inter‐subband scattering play important roles in electron transport. The higher subbands contribute 26% to room‐temperature electron mobility. Two simplified POP scattering models, which either ignore multi‐subband occupation or simplify the in‐scattering processes are evaluated. The results show that both simplified models introduce significant deviations in the mobilities that are limited by POP scattering. The relative magnitudes of mobility in each subband depend on the energy dependence of momentum relaxation time and the energy distribution of each subband.This article is protected by copyright. All rights reserved.