There can be included a variety of uncertainties in all measurement results whether we can perceive or not on the causes. These uncertainties may end up in lowering the reliability of measurement results and also deteriorate the level of quality. For the purpose, we tried to combine the strengths of measurement uncertainty and measurement system analysis together to present a practical flowchart so as to verify those potential variation factors in general measurement processes. As a case study, we did an experiment and gathered data on the length between two holes of an engine cylinder head which is a core part for vehicles with a coordinate measuring machine and estimated nine uncertainty factors of it. Consequently, it was identified that the four primary factors among the nine which were related to the measurement standard, random errors or spread of the repeat measurements, differences between the coefficients of thermal expansion and the environment especially had been the influence around the laboratory. Since it is impossible to analyze the equipment and appraisal variations respectively through the only measurement uncertainty, we have used the measurement system analysis following the flowchart. Showing the result of being just about 0.5 % lower for the appraisal variation, and the equipment variation occupied about 7% for the total Gage R&R. Through this research, we have come to a conclusion that much more detail analysis on variation factors can be possible to be identified in measurement processes by using the developed flowchart which is composed of measurement uncertainty and measurement system analysis. Therefore, we expect engineers who are involved in quality and measurements to utilize this developed method.