Chitosan (CS) has generated considerable interest for its desirable properties and wide applications. Hydrogel has been proven to be a major and vital form in the applications of CS materials. Among various types of CS hydrogels, physical cross-linked CS hydrogels are popular, because they avoided the potential toxicity and sacrifice of intrinsic properties caused by cross-linking or reinforcements. Alkaline solvent system and acidic solvent system are two important solvent systems for the preparation of physical cross-linked CS hydrogels, and also lay the foundations of CS hydrogel-based materials in many aspects. As members of physical cross-linked CS hydrogels, gel material via alkaline solvent system showed significant differences from that via acidic solvent system, but the reasons behind are still unexplored. In the present work, we studied the difference between CS hydrogel via alkaline system and acidic system, in terms of gelation process, hydrogel structure and mechanical property. In-situ/pseudo in-situ studies were carried out, including fluorescent imaging of gelation process, which provided dynamic visualization. Finally, the reasons behind the differences were explained, accompanied by the discussion about design strategy based on gelation behavior of the two systems.