A method of manufacturing a micro flux gate sensor and a micro flux gate sensor manufactured according to the method are provided. The method includes operations of forming a lower coil portion of an excitation coil and a magnetic field detecting coil on a wafer, forming connection portions with a certain height at predetermined positions of the lower coil portion, forming a first insulation layer to cover the lower coil portion and the connection portions, forming a magnetic core on the first insulation layer, forming a second insulation layer to cover the magnetic core and forming an upper coil portion electrically connected to the connection portions to form the excitation coil and the magnetic field detecting coil, and forming a third insulation layer to cover the upper coil portion.