The invention belongs to the field of compliance control over robots, and particularly discloses a compensation-based compliance control system and method for series elastic actuators. The method comprises the following steps of obtaining l according to an impedance model P and the preset target positions/angles l of load ends of the series elastic actuators at the current moment; obtaining delta l according to inverse nominal models P<-1> of load dynamic models of the series elastic actuators and the actual positions/angles l of the load ends of the series elastic actuators at the current moment; obtaining delta l according to l and l; and calculating to obtain l

according to l and P<-1>, calculating the actual target positions/angles l of actuation units at the current moment t based on delta l, delta l and l

, and finally controlling the actuation units of the series elastic actuators to track the actual target positions/angles l in real time so as to realize real-time tracking of the target impedance by the series elastic actuators. The control system and method have the advantagesof being capable of realizing the compliance control over the series elastic actuators, high in control precision, good in effect and the like.