The active power filter (APF) is a new type of power electronic device with the functions of dynamic harmonic suppression and reactive power compensation. The accurate and rapid detection of current harmonics in real time is an important part of determining the performance of APF. The fast Fourier transform (FFT) is a widely used harmonic detection method. However, the conventional FFT algorithm is complicated in calculation, has time delay, poor real-time performance, and is easily affected by grid voltage waveform distortion or frequency fluctuation, which affects the accuracy and efficiency of harmonic detection, thereby reducing the compensation effect and comprehensive performance of APF. Therefore, this paper proposes an APF harmonic detection and compensation strategy based on split-radix FFT algorithm. Through butterfly operation, the radix-2 algorithm is used for the input of even numbers, and the radix-4 algorithm is used for the input of odd numbers, effectively reducing the complexity of the FFT algorithm, enhancing the real-time detection of harmonics. The split-base FFT algorithm is optimized by using Kaiser window to improve the harmonic detection accuracy and anti-interference ability of harmonic detection, ensuring the harmonic detection and compensation effects and overall performance. The correctness and effectiveness of the proposed harmonic detection strategy are verified by the three-phase four-wire APF prototype experiment, and the conditioning time to re-reach the new steady-state can be shortened by 25% in the case of sudden load changes.