In order to analyze the accuracy of three-dimensional coordinates transformation and guide the distribution of common points in measurement on site, a mathematical model of the relationship between the accuracy of three- dimensional coordinates transformation and common points was established using least square estimation of unequal accuracy theory. Analyzing the model, we could get the transformation accuracy at any point of the space and draw a conclusion that the mean square error and distribution of the common point are the main factors of coordinate transformation accuracy. Finally, the factors of coordinate transformation accuracy were analyzed using three-dimensional coordinate measurement data of common points. The experiment shows that transformation accuracy can be effectively improved by improving the measurement accuracy of the laser tracker and changing the distribution of the common point.