In order to improve the precision of CNC machine tools effectively, a method for modeling and predicting their spatial errors based on spatial feature points was proposed. Taking three-axis vertical CNC machine tools as the research object, we think that the whole space formed by machine tools’ working can be seen as the combination of a number of cubes, whose vertices are considered to be feature points, and others in the cubes are called nonfeature points. So, each nonfeature point’s errors can be predicted by the cube’s eight vertices’ errors. Based on the above ideas, an approach including the installing instrument for measuring any spatial feature point’s errors was put forward. In this way, all data of the feature points’ errors could be obtained. Moreover, according to these error data, the prediction model of nonfeature points’ errors was established by using the internal division ratio method. The method has the advantages of small interpolation operation, easy integration in the numerical control system, and high compensation precision. Finally, an example was used to prove its effectiveness and feasibility.