The grazing incidence X-ray reflection spectra of a Mo/Si multilayer annealing at a temperature of 250 ℃ at different time are measured and the relative shifts in Bragg peak positions are extracted, from which the relative period thickness changes of the Mo/Si multilayer at pm-accuracy are calculated by fitting Bragg formula. A diffusion limited model is applied to account for the growing interfaces between Mo and Si, which states that the thickness of a compound interface grows quadratically over time. From this model the diffusion constant figures out to be 0.33×10-22 cm2/s. Then the grazing incidence X-ray reflection spectra are fitted by genetic algorithm using four-layer model, with the densities of Mo, Si and MoSi2 determined to be 9.3, 2.5 and 5.4 g/cm3. Accordingly, the diffusion constant is modified to be 1.88×10-22 cm2/s, which gives a quantitative criterion for investigating the thermal stability of the Mo/Si multilayer.