Focusing on the underdeveloped robustness when the existing extended rough set model encounters the noise for the incomplete information system, the necessity of adjusting the size of basic knowledge granule as well as introducing the relative degree of misclassification was analyzed. Then the Variable Precision Rough Set model based on Variable-Precision Tolerance Relation (VPRS-VPTR) was established on the basis of the object connection weight matrix, which was proposed according to the lack probability of system attribute value. Moreover, the properties of the VPRS-VPTR model were discussed, the classification accuracy under the basic knowledge granule size and the relative degree of misclassification was analyzed, the corresponding algorithm was depicted and the time complexity analysis was given afterwards. The experimental results show that the VPRS-VPTR model has higher classification accuracy compared with some other research about the expanded rough set, and the change trend of the classification accuracy is similar for the train set and the test set of several groups of incomplete data sets in UCI database. It proves that the proposed model is more precise and flexible, and the algorithm is feasible and effective.