The protoberberine alkaloids, exampled by berberine, have abundant biological activities, which show excellent anti-inflammatory effects in a variety of inflammatory diseases such as epilepsy and cardiovascular and cerebrovascular diseases. Due to the challenge in separation and purification of protoberberines from natural resource and intrinsic low bioavailability, many researchers have devoted to the discovery of new total synthesis methods or structural modification. The total synthesis, anti-inflammatory pathway and anti-inflammatory structure-activity relationships of protoberberine skeleton are summarized for the discovery of de novo protoberberine chemotypes with anti-inflammatory activity.