In order to reduce the error of energy metering, an electric energy metering method is proposed while inter-harmonic exists. First, some deficiency of current electric energy metering method is analysed, then power formula is presented, and an improved algorithm based on Pisarenko is proposed. Frequency and amplitude components can be extracted by traditional Pisarenko algorithm accurately, but phase information can not be extracted. This paper presents an improved algorithm based on Pisarenko. The simulation results show that Pisarenko algorithm can identify parameters for each frequency component of the electrical signal accurately, especially phase information, filter out false frequency component and have a strong anti-jamming capability. Budeanu power definition that considered the direction of flow is used in power calculation. Finally, the influence to customers and power enterprises is analyzed by use of the measurement method based on this paper. The result shows that the new measurement method is suitable for energy metering while inter-harmonic exists.