The microstructure of the pectin/whey protein isolate mixtures under incompatible conditions was investigated using dynamic light scattering spectroscopy, transmission electron microscopy and shear-viscosity model. Under the condition of 90 ℃ and pH 7.4, the presence of negatively charged pectin could induce depletion aggregation in a 5% protein solution, and promote phase separation; precisely, when the mass ratio of pectin/whey protein isolate was lower than 0.08, the hydrodynamic size of the aggregates was less than 300 nm, and the system showed Newtonian properties; when the mass ratio was higher than 0.08, the viscosity of the solution increased rapidly, the shear thinning properties became obvious and the size of the aggregates was close to 700 nm.