Boron-dipyrromethene (BODIPY) derivatives are prospective organic-based triplet photosensitizers. Since the triplet generation yield of the parent BODIPY is low, heavy atoms are widely used to improve the triplet yield. However, the dimerization of BODIPYs can also significantly improve their ability to produce triplets. Through a comparative study of the triplet formation dynamics of two heavy-atom-free orthogonal covalent BODIPY heterodimers that differ in their dihedral angles, we have demonstrated that the mechanism of spin-orbit charge-transfer intersystem crossing (SOCT-ISC) promotes the triplet generation of BODIPY heterodimers in solution. Different from the general understanding of SOCT-ISC, the heterodimer with a smaller dihedral angle and low structural rigidity showed better triplet generation due to (a) the stronger inter-chromophoric interaction in the heterodimer, which promoted the formation of a solvent-stabilized charge-transfer (CT) state, (b) the more favorable energy level alignment with sizeable spin-orbit coupling strength, and (c) the balance between the stabilized singlet CT state and limited direct charge recombination to the ground state in a weakly polar solvent. The complete spectral characterization of the triplet formation dynamics clarified the SOCT-ISC mechanism and important factors affecting the triplet generation in BODIPY heterodimers.