A high accurate electronic instrument transformer calibration system is introduced in this paper. The system uses the fourth-order convolution window algorithm for the error calculation method. Compared with Fast Fourier Transform, which is recommended by standard IEC-60044-8 (Electronic current transformers), it has higher accuracy. The relative measuring errors caused by asynchronous sampling could be reduced effectively without any special hardware technique adopted. The results show that the ratio error caused by asynchronous sampling can be reduced to 10-4, and the phase error can be reduced to 10-3 degrees when the deviation of frequency is within ±0.5 Hz. The present method of measurement processing is achieved by a high-accuracy USB multifunction data acquisition (DAQ) card and virtual measurement devices, with low cost, short exploitation period and high stability.