Magnetotransport properties of In0.53GaAs/In0.52AlAs high electron mobility transistor (HEMT) structures with different channel thickness of 10—35 nm have been investigated in magnetic fields up to 13 T at 1.4 K. Fast Fourier transform has been employed to obtain the subband density and mobility of the two-dimensional electron gas in these HEMT structures. We found that the thickness of channel does not significantly enhance the electron density of the two-dimensional electron gas, however, it has strong effect on the proportion of electrons inhabited in different subbands. When the size of channel is 20 nm, the number of electrons occupying the excited subband, which have higher mobility, reaches the maximum. The experimental values obtained in this work are useful for the design and optimization of InGaAs/InAlAs HEMT devices.