The purpose of this study is to empirically analyze the productivity change of the 10 Single PPM Certification Company in the 3 Industry(Electronics, Motor-Parts, Machines). In this study, Productivity change over the time in Korean small and medium sized firms in the 3 industries by the bootstrapped Malmquist Productivity Index(MPI). The traditional Malmquist Productivity Index(MPI) and Data Envelopment Analysis(DEA) Models have not only bias but also lack statistical confidence intervals. they could lead to wrong evaluations of the efficiency and productivity scores. In this paper, DEA and a MPI are combined with a bootstrap method in order to provide statistical inferences that analyze the performance of the Single PPM Certification Company. The data cover the period between 2004 and 2007. The result of this paper reveals : 1) The Electronics Industry had productivity effect of 17%, but there was not direct effect for other Industries(Motor-Parts, Machines). 2) average productivity Progress of the 7DMU(Electronics), 1DMU(Motor-Parts) and none(Machines).