If a signal is analyzed by using FFT algorithm under nonintegerperiod sampling condition, it will cause spectral leakage, and cause measurement error of active electric energy. After defining fundamental active electric energy and harmonic active electric energy, and proving that there is a certain relationship between the total electric energy consumed by loads and the spectrum of voltage and current signals, the harmonic subgroup windowed FFT algorithm is proposed. Firstly, it groups the spectrum bins of the windowed signal using the harmonic subgroup grouping method in IEC standard. Then, the electric energy recovery coefficient is calculated based on the rule that the total active electric energy remains unchanged after the signals is windowed. Lastly, fundamental electric active energy and harmonic electric active energy is obtained using the coefficient and the harmonic subgroup bins’ parameters. Numerical simulation analysis and actual evaluation show that the new algorithm uses Hanning window to process the signals, it can achieve higher accuracy to calculate fundamental electric active energy and harmonic electric active energy.