The sampling nonlinear deviation is caused by device difference in the acquisition circuit and specific nonlinear of measured source, in order to improve the accuracy of the acquisition, use high order polynomial fitting algorithm in multi - channel acquisition system. Design a filter for the specific frequency on the hardware acquisition circuit and adjustable amplifier circuit. The deviation caused by the difference of the device was corrected under given value condition. At the same time, through the method of software compensation, the high order polynomial fitting algorithm was used to solve the nonlinear deviation of full range. The results show that the maximum signal deviation between the channels is no more than ±1% of the signal average value, the combination of hardware and software ensured that the high precision requirements of acquisition system in the entire range. It provides a solution and reference to the high precision acquisition system, which is a combination of software and hardware.