The invention discloses a flexible temperature sensor comprising a microstructure and a preparation method, the flexible temperature sensor comprising the microstructure comprises a substrate, a first flexible layer, a conductive layer and a second flexible layer which are sequentially arranged from bottom to top, the substrate is provided with a conical microstructure, the conical microstructure is integrally formed on the substrate, the first flexible layer is arranged on the substrate, and the conductive layer is arranged on the second flexible layer. The top of the conical microstructure protrudes out of the second flexible layer, the conductive layer comprises a temperature sensor and an output assembly used for outputting a temperature signal, the output assembly comprises a temperature signal interface and a temperature signal output wire, one end of the temperature signal output wire is connected with the temperature signal interface, and the other end of the temperature signal output wire is connected with the temperature sensor. The flexible temperature sensor has high fitting degree with the skin, does not generate motion artifacts, and improves the accuracy of monitoring signals of the flexible temperature sensor.