The invention relates to a non-continuous machining surface system error and random error separation method and belongs to the mechanical machining field. The objective of the invention is to solve the incapability of an existing method to be applied to non-continuous surface error separation. The method includes two steps, namely preliminary separation of system error and random error and precise separation of the system error and the random error. According to the method, the system error is obtained from non-continuous machining surface profile error through gridding and interpolation fitting, and differencing is performed on the surface profile error and the system error, so that the random error can be obtained, and a preliminary separation result can be obtained; and the number of grids is increased continuously, so that the separation result of the system error and the random error is considered as a precise separation result when the information entropy of the system error is stable. The method of the invention is suitable for error separation of non-continuous machining surfaces with holes and slots. The method has the advantages of high error separation efficiency and accurate separation result.