The control in transient conditions when hydraulic brake and regenerative brake switch mutually is the key technical issue about electric vehicle hybrid brake system, which has a direct influence on the braking feel of driver and vehicle braking comfort. A coordination control system has been proposed, including brake force distribution correction module and motor force compensation module. Brake force distribution correction module has fixed the distribution results in hydraulic brake force intervention condition, hydraulic brake force evacuation condition and regenerative brake force low speed evacuation condition. Motor compensation module has compensated hydraulic system with motor system, which has fast and accurate response, thus the response of whole hybrid system has been improved. Simulation results in transient conditions show that the coordination control strategy can effectively reduce the fluctuations and deviations of total brake force, and improve braking feel of driver and vehicle braking comfort.