To analyze the intrinsic relationship among the geometric deviations of machined free-form surfaces, a spatial statistical analysis method was applied to decompose these deviations into deterministic and random deviations, which would help to determine error sources. The B-spline method was applied to iteratively build a surface that forms deterministic deviations. And the MoranI was used to test the spatial statistical characteristics of the model residuals in every iterative step. If the residuals were spatially independent, then they might present the random deviations. To verify the presented method, the geometric deviations on a CNC machined free-form surface were successfully decomposed into the deterministic and random deviations.