A system for determining the thermal properties of rocks under high pressure conditions in deep sea includes a first pressure vessel having a data collecting unit and a second pressure vessel having a chamber being filled with seawater, communicating with a drain valve, and having a rock sample disposed therein. First and second temperature sensors are respectively disposed in the center and on the surface of the rock sample. A third temperature sensor and a pressure sensor are disposed in the chamber. Outputs of the temperature sensors and the pressure sensor are communicated with inputs of the data collecting unit via watertight cables. Determining the thermal properties of rocks under high pressure conditions in deep sea includes rapidly opening the drain valve for instant loading of the rock sample and introducing an established finite element numerical inversion model. No heat source for electrical heating nor booster pump is needed.