Charge transfer and recombination across the inorganic/organic interface in nanocrystal or quantum dot (QD)-molecule hybrid materials have been extensively studied. Principles of controlling charge transfer and recombination via energetics and electronic coupling have been established. However, the use of electron spin to control transfer and recombination pathways in such systems remains relatively underexplored. Here we use CdS QD-alizarin (AZ) as a model system to demonstrate this principle. Using time-resolved spectroscopy, we found that the charge-separated states (QD(-)-AZ(+)) created by selectively exciting AZ molecules mostly recombined to regenerate ground-state complexes, whereas apparently the "same" charge separated states created by exciting QDs recombined to produce AZ molecular triplet states. Such a difference can be traced to the distinct spin configurations between excited QDs (QD*, with an ill-defined spin) and AZ ((1)AZ*, spin singlet) and the asymmetric electron and hole spin-flip rates in II-VI group QDs. The transferability of such a principle was confirmed by similar observations obtained for CdS QD-tetracene complexes. Opening an avenue for controlling charge transfer and recombination pathways via electron spin is potentially important for applications such as artificial photosynthesis.