The invention provides a temperature control module in a biological reaction instrument, the temperature control module comprises a flat plate and an upper cover, the upper cover and the flat plate are oppositely arranged and connected into a whole, a plurality of container holes for placing reaction consumables are formed in the upper cover, a containing cavity is formed between any two adjacent container holes on one side, facing the flat plate, of the upper cover, the containing cavities communicate with one another and are filled with a phase change heat transfer medium. Due to the adoption of the phase change heat transfer medium, the temperature increasing and decreasing rate is increased, the temperature uniformity of the temperature control module in the biological reaction instrument can be remarkably improved, the biochemical reaction time can be shortened, and due to the fact that the structure in the prior art is not adopted any more, the temperature regulation performance of the temperature control module in the biological reaction instrument does not excessively depend on the machining and assembling precision of related parts, so that the reliability of the module is improved.