Zwitterionic polymers are characterized with equal anion and cation groups on the molecular chains, which make them highly hydrophilic and antifouling. They can resist nonspecific protein adsorption, bacterial adhesion, and biofilm formation. Therefore, they have great potential to be applied in a wide range of biological and medical related fields, such as antifouling coatings of biomedical implants, blood contacted sensor and drug delivery in vivo, separation membrane and marine coatings. The review mainly focuses on the progress of those applications of zwitterionic polymers on the molecular level. Problems existed in these applications are also discussed and the development of in future is prospected.