The invention discloses an STM-BJ-based monomolecular junction thermoelectric potential measurement method and STM-BJ-based monomolecular junction thermoelectric potential measurement equipment. A Seebeck coefficient of a molecular junction is obtained by acquiring a single molecule, verifying the single molecule, measuring a thermal voltage, verifying the single molecule, repeatedly acquiring a plurality of pieces of data, and then carrying out corresponding statistics and calculation. A stable and easily-adjusted heat source is provided for a substrate based on an STM-BJ technology, so thatthe temperature difference is constructed at the two ends of the molecular junction, an independent voltage amplifier is introduced to measure the electromotive force generated by the temperature difference after the molecular junction is formed, and therefore measurement of the thermoelectric potential of the monomolecular junction is achieved. Compared with an MCBJ technology and an STM-BJ needle tip temperature control technology, the research means has the advantages of being simple, efficient, wide in adjustable range, high in error-tolerant rate and the like, the measurement efficiency of the monomolecular junction thermoelectric potential is greatly improved, research and development of a novel organic thermoelectric material are promoted, and powerful assistance is provided for thesociety where the energy urgently needs to be changed.