The site preference, electronic structure, and magnetism of Heusler alloy Fe2RuSi are investigated theoretically and experimentally. The magnetic and electronic properties of Heusler alloys are strongly related to the atomic ordering and site preference in them. Usually, the site preference of the transition metal elements is determined by the number of their valence electrons. However, the recent results suggest that some new possible factors such as atomic radius should also be considered. Here we compare the phase stabilities of several different atomic orderings like XA, L21, DO3, L21B in Fe2RuSi, in which Fe and Ru atom have 8 valence electrons each, thus the influence of number of their valence electrons can be omitted. First-principles calculations suggest that Ru atom prefers entering sites A and C in the lattice. In ground state, the most stable structure is of XA type, in which Fe and Ru atoms occupy A and C sites, respectively and the second stable structure is L21B type, in which Fe and Ru atoms occupy A and C sites randomly. With Ru atom entering into the B site, the total energy increases rapidly. Thus there is still a strongly preferable occupation of Ru though Fe and Ru atom are isoelectronic. This confirms that the valence electrons rule may be not enough to determine the site preference of the transition metal element in Heusler alloy. The preferable occupation of Ru atom in Fe2RuSi can be explained from the electronic structure. It is found that in the XA DOS, there is strong hybridization between the electrons of the nearest Ru and Si or Fe (B) atom. However, in the high energy L21 structure the hybridization between Ru and the nearest Fe (A, C) is weak, which reduces its phase stability. This is confirmed further by the charge density difference calculation. Single phase Fe2RuSi with a lattice parameter of 5.79 is synthesized successfully. Comparing the superlattice reflections (111) and (200) in the experimental XRD pattern with those in the simulated patterns for different structures, we find that Fe2RuSi crystallizes in L21B structure rather than the most stable XA one at room temperature, which mainly originates from the contribution of mixed entropy to the free energy, and its caused atomic disorder at high temperatures. This disorder can be retained during the cooling procedure, while it does not influence the conclusion that Ru atom prefers the (A, C) sites in Fe2RuSi strongly. Finally, the saturation magnetization Ms at 5 K is 4.87 B/f.u., which agrees well with the theoretical result. The large total magnetic moment mainly comes from the contributions of Fe, especially Fe magnetic moments on B sites.