Firstly,the electronic structure of β-FeSi2 and the density of states (DOS) of subshells of Fe and Si were calculated. The calculations were carried out using the self-consistent full-potential linearized augmented plane wave method within the density functional theory. The general gradient approximation was used to treat the exchange and correlation potential. The DOS of β-FeSi2 is mainly composed of d-shell electrons of Fe and p-shell electrons of Si. Secondly,the stable atomic substitution positions of doping atoms were determined by calculating the total energies for Fe1-xCoxSi2 and Fe(Si1-xAlx)2. The Fe atom at the FeⅡ position and the Si atom at the SiⅠ position were preferentially substituted by Co and Al,respectively. This preferential substitution is in good agreement with results of the existing publications. Finally,the elctronic structures of Fe1-xCoxSi2 and Fe(Si1-xAlx)2 were calculated and analyzed as well. The intrinsic relations between electronic structures of Fe1-xCoxSi2 and Fe(Si1-xAlx)2 and their respective thermoelectric properties including Seebeck coefficient,electric conductivity and thermal conductivity were discussed in detail.