Abstract A FFT algorithm with the DSP processor based on TMS320C5402 and fluorescence thermal measurement based on DSP are proposed. Basing on the Fast Fourier transform (FFT), the fluorescence lifetime is obtained from the tangent function of the phase angle of the first non-zeroth items of the FFT result. This method has a series of advantages such as quick calculation, high accuracy and immunity to the base signal, so the stability, real time and speediness of fluorescence thermal measurement system can be advantaged.