Singlet fission (SF) is an appealing process where one photoexcited singlet transforms to two triplets, which can overcome thermalization energy loss and improve solar cell efficiency. However, it remains unclear how intermolecular coupling, which is subject to molecular stacking, controls SF pathways and dynamics. Here, we prepared polymorph rubrene single crystals with different stacking geometries, including orthorhombic (Orth.), triclinic (Tri.), and monoclinic (Mono.) phases. By micro‐area ultrafast spectroscopy, we find that Orth. and Tri. phases with closer π‐π stacking exhibit co‐existing coherent and incoherent SF channels while loosely stacked Mono. phase shows only incoherent SF. Furthermore, incoherent SF is thermally activated in Orth. but barrierless in Mono. and Tri. phases. Quantum mechanical calculation reveals that different electronic coupling strength in different phases leads to different SF dynamics. This study demonstrates that molecular stacking governs SF dynamics through electronic coupling, providing guidance for designing efficient SF materials via crystal structural engineering.