In molecular thermoelectrics, the thermopower of molecular junctions is closely interlinked with their thermal properties; however, the detailed relationship between them remains uncertain. This study systematically investigates the thermal properties of self-assembled monolayer (SAM)-based molecular junctions and relates them to the thermoelectric performance of the junctions. The electrode temperatures for the bare Au-TS, Au-TS/EGaIn, and Au-TS/TPT SAM//Ga2O3/EGaIn samples placed on a hot chuck were measured under different conditions, such as air vs vacuum and the presence and absence of thermal grease, which generates a heat conduction channel from a hot chuck to gold. It was revealed that the SAM was the most efficient thermal resistor, which was responsible for the creation of a temperature differential (Delta T) across the junction; Delta T in an air atmosphere is overestimated to some extent, and air mainly contributes to large dispersions of thermovoltage (Delta V) data. While junction measurements in air were possible at low Delta T (up to 13 K), the new optimal condition, under a vacuum and with thermal grease, allowed us to examine a wide temperature range up to Delta T = 40 K and obtain a more reliable Seebeck coefficient (S, mu V/K). The value of S under the new condition was similar to 1.4 times higher than that measured in air without thermal grease. Our study shows the potential of liquid-metal-based junctions to reliably investigate heat conduction across nanometer-thick organic films and elaborates on how the thermal properties of molecular junctions affect their thermoelectric performance.