Now a days, as a mass-storage USB becomes comfortable to carry, function of USB is being developed fast. However, there is a problem that the personal information which is stored in USB could be exposed being used with negative purpose without other certification process. This paper suggests OTP(One-Time Password)-based certification protocol of USB to securely protect personal information stored in USB without additional certification information. The proposed OTP based certification protocol of USB not only demands low calculations but also prevents physical approach of USB of other network and does not allow unnecessary service access of user because it conducts simple action and uses one-way hash function. Therefore, communication overhead and service delay is improved. In the experiment, the proposed protocol compares and evaluates throughput of certification server according to the numbers of USB and delay time of packet certification with a device(USB driver) which simply save device and a device(USB Token) which can calculate by oneself. As a result, it is improved as the number of 12.5% in the certification delay time on average and is improved as the number of 10.8% in the throughput of certification server according to the numbers of USB.