Chitosan microgels (h-CSMs) were prepared by cross-linking hydrophobically modified chitosan with sodium phytate (SP). Emulsions stabilized by h-CSMs with different inter-phase fraction, microgel concentration and cross-linking density were studied of their microstructural and rheological properties. In particular, the large amplitude oscillatory shear (LAOS) of the high internal phase emulsions (HIPEs) stabilized by h-CSMs were systematically analyzed using the Fourier transform with Chebyshev polynomials (FTC) and sequence of physical processes (SPP) methods to explore their nonlinear rheological properties. It was found that the HIPEs showed Type III LOAS response with weak strain overshoot depending on the emulsion parameters and microgel characteristics. The FTC method enabled the extraction of nonlinearity measures at limiting conditions (γ → 0, γ → γ