This paper investigates a human-machine cooperative trajectory planning and tracking control approach for automated vehicles. The proposed method is developed based on a novel algorithm of cooperative human-machine rapidly-exploring random (HM-RRT) for path planning, together with the risk assessment of driver behavior. First, the driver's behaviour is assessed according to the information of the predicted vehicle trajectory, the identified safe driving area and the driving risks evaluated in both lateral and longitudinal directions. Based on the driver's expected driving task, when driving risks are identified by real-time assessment, then the human-machine cooperation is activated during trajectory planning. By HM-RRT, the newly developed safety assurance mechanism for path planning, the cooperative trajectory is then generated, which incorporates the driver's desire and actions and automation's corrective actions, to ensure the safety, stability and smoothness of the human-vehicle system. The simulation and experimental results show that the proposed HM-RRT algorithm can effectively improve the convergence rate and reduce the computation load, comparing to the conventional method. Beyond this, the proposed human-machine cooperation approach is able to simultaneously ensure the safety, stability and smoothness of the vehicle and largely reduce human-machine conflicts in real-time applications, demonstrating its feasibility and effectiveness.