Among donor molecules labeling protein in living cells to be measured, the rate of donor molecules binding to an acceptor molecule and occurring FRET is determined. In a plurality of previous measurement samples having different ratios of first molecule concentration to second molecule concentration, a fluorescence lifetime of the first molecule are calculated and the fluorescence lifetime minimum value of the first molecule is calculated. The samples are irradiated with a laser beam having time-modulated intensity and the fluorescence emitted by the laser-irradiated measurement samples are measured. By using the fluorescent signals thus measured, the fluorescence lifetime of the first molecule is calculated. By using the fluorescence lifetime minimum value of the first molecule and the fluorescence lifetime of the first molecule that is calculated above, the rate of the first molecules occurring FRET in the first molecules in the measurement samples is calculated.