The invention relates to a fluxgate sensor and a manufacturing method thereof. According to the method, the film growth technology is utilized to generate a soft-magnetic material layer (a permalloy film) taken as a magnetic core on a surface of an insulation substrate; after an insulation layer is formed on the soft-magnetic material layer, a metal conduction layer is deposited, permalloy molecules can be artificially arranged through the film growth technology, and high precision control on uniformity and thickness is realized; the etching technology is utilized to etch the alloy film into an excitation coil and an induction coil, the flow is monitored by apparatus equipment, and the nano-level fluxgate sensor is formed. The method is advantaged in that manpower is saved, the speed is quick, efficiency is high, a defect rate is low, manpower cost is substantially saved after one-time investment, and the fluxgate sensor has advantages of small volume, high precision, quite low power consumption, high sensitivity, mass-batch production and high yield.