Calcium sulfoaluminate cement (CSA) has been widely applied in marine civil engineering projects due to its high Cl- binding capacity, which has been proved but not thoroughly explored. In-depth understanding on its hydration process and binding mechanism is the key step to guarantee its service durability. Up to date, most previous researches focused on hydration and binding mechanism on external ingress Cl-, while only limited cases worked on those with premixed Cl- introduced by raw materials. Within CSA mixes, gypsum plays an important role on its hydration and hardened properties. Therefore, it is greatly needed to reveal the effects of gypsum and premixed Cl- on hydration and binding mechanism for CSA. In this paper, a series of experiments, including analysis on mineralogy quantification and testing indicators related to the binding properties, were carried out. Systematic results showed that the binding mechanism of premixed Cl- was similar with that of the ingress Cl-, i.e., the premixed Cl- transformed into Friedel’s salt by reacting with hydration products, such as Al-Fe-mono (AFm). Besides, gypsum induced the formation of AFt at the early stage of hydration so that early compressive strength was improved but AFt did little contribution to binding Cl-. On the other hand, premixed Cl- in CSA shortened the setting time, promoted the process of hydration heat, and effectively inhibited the generation of microcracks. More noteworthy, calcium aluminate hydrates (i.e., CAH10 and C3AH6) generated by CSA also made a significant contribution to Cl- binding in addition to AFm.