The process of extracting small molecular ingredients from biological materials under super high pressure is a process which makes use of super high pressure to extract small molecular active ingredients from biological materials, especially natural products, which mainly consists of extracting the mixture of solid raw material and extraction solvent under increased pressure. Said process comprises the following steps: the step of pretreatment, crash and formulation; the step of closure, charging the formulated mixture of raw material and extraction solvent into high pressure container, then closing the high pressure container; the step of increasing pressure, increasing the pressure of the high pressure container from 100 Mpa to the predefined pressure of 1000 Mpa; the step of holding pressure, holding the predefined pressure for 3-30 minutes; the step of releasing pressure, releasing the pressure of the high pressure container to normal pressure, removing the mixture. The present invention modifies the traditional extraction process of small molecular ingredients in biological materials, which not only makes extracts avoiding heating, but also has the advantages of high extraction yields, rapid extraction and broad extraction solvents.