We apply first-principles approaches to investigate the spin (charge) Seebeck effects [Ss(c)] and spin (charge) thermoelectric figure of merits [ZTs(c)] of manganese-phthalocyanine spin-polarized scanning tunneling microscopy (MnPc SP-STM) junctions. The magnetic tunneling junctions are N-type junctions because their Sc values are negative. Their Ss and Sc values are sufficiently large for the efficient generation of measurable spin and charge currents. ZTs(c) values strongly depend on the competition between electron and phonon thermal conductances: ZTs(c) ∞ Ss(c)2 for κph ≥ κel, and ZTs(c) ∞ Ss(c)2κel for κel ≥ κph. Ss changes signs when the spin-valve junction rotates its magnetic structure from the antiparallel (AP) to the parallel (P) configuration. This behavior indicates that spin-current direction can be reversed by alternating magnetic configurations between AP and P states. Spin-current dissipation in the junctions is minimized because the sizes of the junctions are considerably smaller than the lengths of spin-flip scattering and spin dephasing. The low spin-current dissipation of the junctions suggests that they have potential applications in spintronics and renewable energy. The present finding provides a new approach to spin-current generation through the use of SP-STM based on temperature difference and to controlling spin-current direction through magnetic configurations. The integration of numerous single-molecule magnetic junctions as building blocks into a high-density device is a promising strategy for generating a considerable net spin current for applications in molecular spin caloritronics.