By applying Wannier-based extended Kugel-Khomskii model, we carry out first-principles calculations and electronic structure analysis to understand the spin-phonon coupling effect in transitionmetal perovskites. We demonstrate the successful application of our approach to SrMnO3 and BiFeO3. We show that both the electron orbitals under crystal field splitting and the electronic configuration should be taken into account in order to understand the large variances of spin-phonon coupling effects among various phonon modes as well as in different materials. PACS numbers: 75.85.+t, 77.84.Lf Spin-phonon coupling (SPC) is an important physical effect of multiferroic materials [1], in which the cross couplings between structural distortions and magnetic orderings are closely associated with their key functionalities, such as magnetoelectric coupling and magnetodielectric response. Due to its fundamental and technological importance, the SPC effect is currently under intense scientific investigations [2][3][4][5].The mechanism in realizing SPC is not obviously accessible since the structural distortion, in particular the development of ferroelectricity (FE), does not necessarily induce a change of the magnetic interaction of the material. SPC can be realized by the relativistic effect through the spin-orbital interaction. FE can be induced by the spin spiral structure that breaks the inversion symmetry [6], or the crystal structure in improper multiferroics can be compatible with spin configurations generating the weak ferromagnetism (FM) [7,9,10]. Unfortunately, the resulting electric and magnetic moments are generally small. Recently, a new SPC mechanism has been discovered in ABO 3 perovskites, in which A or B is magnetic transition metal [11][12][13][14][15][16][17][18]. It was found that the low-lying phonon modes, particularly the polar ones, are significantly softened when the spin coupling is changed from being antiferromagnetic (AFM) to FM.First-principles calculations have pioneered the search for SPC materials, from which the differences of phonon frequencies between different spin configurations can be predicted. As a result, a number of transition-metal perovskites with SPC effect have been successfully identified [11][12][13]. Notwithstanding the progress in the field, several fundamental properties remain to be understood. First, for a single material, the SPC strength varies significantly among different phonon modes [19][20][21]. Second, SPC is not observed as a general property for multiferroic materials. In particular, BiFeO 3 (BFO) as one of the most studied room temperature multiferroic materials has surprisingly small SPC effect [22,23]. Based on the Goodenough-Kanamori-Anderson (GKA) rules, the metal-oxygen-metal angles are often used to explain the SPC effect [24,25]; however, a phenomenological argument based on the exchange angle only roughly captures the effect. Therefore, it is not either accurate or conclusive. Precise assignments of electronic processes involved in the magnetic exchange ...