The formation of the sigma phase in technologically important materials influences greatly their mechanical properties. Fundamental knowledge on the sigma phase is demanded to understand the phase stability and reasonably control its precipitation. The present work clarifies the atomic bonding characteristics of the binary sigma phase including A-Al (A = Nb, Ta) and transition metal systems (TM-TM) based on the electronic density of states (DOS) and electron localization function (ELF) calculated by using first-principles methods. We show that the atomic bonds of the binary sigma phase exhibit both metallic and covalent characters. The completely ordered A66.7Al33.3 (A = Nb, Ta) sigma compounds bear higher stability than their counterparts with atomic disordering. Besides, for a TM-TM sigma compound, the constituent atom with more electron shells or less valence electrons presents stronger electronic stability. When increasing its atomic occupancy on a specific site, the atomic bonding on the site becomes stronger.