Spin-flip in purely organic molecular systems is often described as a forbidden process; however, it is commonly observed and utilized to harvest triplet excitons in a wide variety of organic material-based applications. Although the initial and final electronic states of spin-flip between the lowest singlet and lowest triplet excited state are self-evident, the exact process and the role of intermediate states through which spin-flip occurs are still far from being comprehensively determined. Here, via experimental photo-physical investigations in solution combined with first-principles quantum-mechanical calculations, we show that efficient spin-flip in multiple donor-acceptor charge-transfer-type organic molecular systems involves the critical role of an intermediate triplet excited state that corresponds to a partial molecular structure of the system. Our proposed mechanism unifies the understanding of the intersystem crossing mechanism in a wide variety of charge-transfer-type molecular systems, opening the way to greater control over spin-flip rates.