Abstract: The subjectivity and redundancy of inputs are key obstacles to the application of software cost estimation models. To overcome these obstacles, this paper proposed a method for using software cost estimation model based on metrics tool. By introducing Instrumental Variables, this method could transfer data collected by the metrics tool to inputs of one cost estimation model automatically. This method not only improved the accuracy and reliability of the estimation results by avoiding the subjectivity of the inputs, but also improved the work efficiency of the estimator by reducing the hand operation of the estimator. The feasibility and validity of the method has been further proved by applying a case study.