The absorption signals of metastable He in HD 209458b and several other exoplanets can be explained via an escaping atmosphere model with a subsolar He/H ratio. The low abundance of helium can be a result of planet formation if there is a small amount of helium in their primordial atmosphere. However, another possibility is that the low He/H ratio is caused by the process of mass fractionation of helium in the atmosphere. In order to investigate the effect of fractionation in the hydrogen-helium atmosphere, we developed a self-consistent multi-fluid 1D hydrodynamic model based on the well-known open-source MHD code PLUTO. Our simulations show that a lower He/H ratio can be produced spontaneously in the multi-fluid model. We further modeled the transmission spectra of He 10830 lines for HD 209458b in a broad parameter space. The transmission spectrum of the observation can be fitted in the condition of 1.80 times the X-ray and extreme-ultraviolet flux of the quiet Sun. Meanwhile, the ratio of the escaping flux of helium to hydrogen, F (He)/F (H), is 0.039. Our results indicate that the mass fractionation of helium to hydrogen can naturally interpret the low He/H ratio required by the observation. Thus, in the escaping atmosphere of HD 209458b, decreasing the abundance of helium in the atmosphere is not needed even if its He abundance is similar to that of the Sun. The simulation presented in this work hints that in the escaping atmosphere, mass fractionation can also occur on other exoplanets, which needs to be explored further.