Design a rail pressure control algorithm for common Rail diesel engine. The new algorithm uses combinatorial auction mechanism to improve the pressure disturbance in complex conditions.It designs a new calibration algorithm based on the segmentation mechanism to reverse the inefficiency of the original algorithms. On the other hand, It improves many aspects of the PID controller based on the features of the diesel engine. The algorithm is verified by simulation experiment. The results prove that the output rail pressure has good tracking and effciency. Besides , it has good stability that the amplitude of fluctuation is less than 1%. All the results proved that its features are consistent with the engine’s requirment of normal running.