Pervaporation is regarded as one of the most promising technologies for desalination due to its extremely low energy consumption and ability to process high salinity solutions. As an easily accessible natural material with various advantages, chitosan is a promising material for pervaporative desalination. However, the research in this regard is scarce, and all existing works only focus on the desalination of NaCl solutions. Since chitosan has the potential to chelate with various ions, its desalination performance for different salt solutions might vary. In this study, we applied chitosan-based membranes to pervaporative desalination for various salt solutions. The effects that feed salts, feed concentration, and temperatures had on their performance were comprehensively investigated. Moreover, two types of chitosan (Chitosan-K and Chitosan-D) were utilized to investigate the impact of chitosan types and confirm the universality of the conclusion. It was found that the feed salts significantly impact the desalination performance of chitosan membrane depending on their chelation level with chitosan polymers, and the cations (rather than anions) of the salts have a more significant effect. The salt rejection was almost complete at all tested conditions, demonstrating chitosan to be a promising material for pervaporative desalination.