We studied the microstructure of physical chitosan hydrogels formed by the neutralization of chitosan aqueous solutions highlighting the structural gradients within thick gels (up to a thickness of 16 mm). We explored a high polymer concentrations range (Cp ≥ 1.0% w/w) with different molar masses of chitosan and different concentrations of the coagulation agent. The effect of these processing parameters on the morphology was evaluated mainly through small-angle light scattering (SALS) measurements and confocal laser scanning microscopy (CLSM) observations. As a result, we reported that the microstructure is continuously evolving from the surface to the bulk, with mainly two structural transitions zones separating three types of hydrogels. The first zone (zone I) is located close to the surface of the hydrogel and constitutes a hard (entangled) layer formed under fast neutralization conditions. It is followed by a second zone (zone II) with a larger thickness (∼3-4 mm), where in some cases large pores or capillaries (diameter ∼10 μm) oriented parallel to the direction of the gel front are present. Deeper in the hydrogel (zone III), a finer oriented microstructure, with characteristic sizes lower than 2-3 μm, gradually replace the capillary morphology. However, this last bulk morphology cannot be regarded as structurally uniform because the size of small micrometer-range-oriented pores continuously increases as the distance to the surface of the hydrogel increases. These results could be rationalized through the effect of coagulation kinetics impacting the morphology obtained during neutralization.