The error measurement method is an essential for further enhancing the machining accuracy of a micro machine tool. An on-machine vision-based measurement method that can measure 2-D contouring-/tracking errors of a micro machining process had been previously developed. An on-machine depth-error measurement method was proposed in this study to fulfill the complete 3-D machining errors measurement. The method adopts image re-constructive technology and camera pixel correction to provide non-contact measurement capability. To improve the measurement limits due to the pixel resolution and the filler of view of a CCD, a 2-step measurement method with use of a depth model was developed. Because of the capability of eliminating the shadow effects caused by the tilting light source, the proposed method provides more accurate and reliable measurement results. Sensitivity analysis was conducted to assess the influence of the CCD setup errors on the measurement accuracy for implementation. Experiment was conducted and the results have shown the effectiveness and feasibility of the measurement method.