Objective To design a global sliding mode control algorithm for the purpose of eliminating the chattering effect in conventional sliding mode control algorithm on both the controller and controlled plant from the conventional sliding mode control algorithm and regulating the intra aorta pump in response to the demand of blood circulation system in human. Methods A dynamic disturbance compensator was used to estimate the uncertainty of the intra aorta pump control system. Computer simulations and in vitro experiments were also conducted to verify the dynamic characteristics and robustness of the controller. Results As the dynamic disturbance compensator was used to estimate the uncertainty of system, the chattering effect in sliding mode control algorithm was eliminated. When the reference flow rate was set at 5 L/min, the response time was 80 ms without any overshot and static error. When the load torque of the controller was increased to 0.4 N·m, the response time was 25 ms. When the pulsatile signal was input as the reference flow rate, the dynamic response time was 80 ms with the maximum error of flow rate being 0.03 L/min. In the in vitro experiments, as the feedback frequency of flow rate signal and pump speed signal were lower than that in the ideal condition, the controller performance was deteriorative compared with computer simulation. The experimental results demonstrated that when the reference flow rate was set at 5 L/min, the response time was 0.26 s with the error of flow rate being 0.1 L/min. Conclusions The controller provided in this paper can accurately regulate the intra aorta pump according to the reference flow rate. Furthermore, it has a strong robustness for the uncertainty and disturbance of the control system. Due to the use of dynamic disturbance compensator, the chattering effect of the algorithm has been eliminated.