We report a first-principles investigation of spin-dependent transport properties in two different graphene-based molecular junctions. By applying different temperatures between two leads without bias voltage, spin-dependent currents are driven which depend on reference temperature T , temperature gradient T , and gate voltage V g. Moreover, pure spin currents without charge currents can be obtained by adjusting T , T , and V g for both molecular junctions. The directions of pure spin currents in these two molecular junctions are opposite, which can be understood by analyzing the transmission coefficients under equilibrium states. Spin thermopower, thermal conductance, and the figure of merit as functions of T , V g , and chemical potential μ were also investigated in the linear response regime. Large spin thermopower and spin figure of merit can be obtained by adjusting V g and μ for each junction, which indicates proper application of spin caloritronic devices of our graphene-based molecular junctions.