Addressing the demands of global waste heat recovery and low-power spin-based information processing, this paper designs and investigates two types of molecular-scale nanodevices composed of the two-dimensional ferromagnetic material Fe₃GeTe₂ and the organic molecule C₈-BTBT with different interfacial coupling modes. The study is based on first-principles density functional theory (DFT) and the non-equilibrium Green’s function (NEGF) method, aiming to reveal the influence mechanism by which interfacial coupling strength influences on the spin thermoelectric transport properties of the devices. The results show that the interfacial coupling strength directly affects interfacial charge transfer and spin transport behavior: the charge transfer amount is 0.766e^– in the strong coupling mode and decreases to 0.256e^– in the weak coupling mode. Under strong coupling mode, the device exhibits high electrical and thermal conductance, whereas under the weak coupling, both charge transport and thermal conductance are significantly reduced. Due to the trade-off between electrical and thermal conductance in thermoelectric performance, the markedly suppressed thermal conductance under weak couplingresults in an increase in the spin figure of merit (ZT) from 0.71 to 3.45. Notably, the study also reveals that interlayer coupling can modulate the distribution of spin charge density. This leads to a significant polarity reversal of the spin current in the molecular device under different coupling modes. In addition, a thermally induced negative differential resistance effect is observed. This study provides a theoretical basis for the development of high-efficiency and tunable spin thermoelectric prototype devices through interfacial coupling engineering.