Measurement process has an important impact on the reliability of measurement. The reliability of measurement is weighed by measurement uncertainty. It is very difficult to estimate the uncertainty in the indirect measurements according to the transfer formula given by GUM (Guide to the Expression of Uncertainty in Measurement). Monte Carlo method was proposed to solve the problem of uncertainty estimation and seek suitable measurement process in the indirect measurements. The mathematical relation between the measurand and the direct measures is established firstly. Then Monte Carlo method was adopted to conduct the sampling and synthesis of measurement uncertainty contributors. At last, the measurement method was evaluated and improved according to Procedure for Uncertainty Management, which is given by next generation of GPS (Geometrical Product Specification). Experimental result shows that Monte Carlo Simulation method has a good application foreground in the uncertainty estimation and measurement process design.