The invention relates to an MEMS flexible manganin-constantan composite ultra-high pressure sensor and a manufacturing method thereof. The composite ultra-high pressure sensor comprises a substrate, wherein the substrate is sputtered with a manganin sensitive element, four first electrodes corresponding to the manganin sensitive element, a constantan sensitive element and four second electrodes corresponding to the constantan sensitive element, an input end and an output end of the manganin sensitive element are respectively connected with the two first electrodes, an input end and an output end of the constantan sensitive element are respectively connected with the two second electrodes, and the surfaces of the manganin sensitive element, the constantan sensitive element, the first electrodes and the second electrodes are covered with an insulating layer; and the manganin sensitive element and the constantan sensitive element adopt spiral centrosymmetric distribution, and both the substrate and the insulating layer adopt a polyimide material. The composite ultra-high pressure sensor has the characteristics of high precision, fast response, large output signal and the like.